From 3e5505fa4de90cdb23f9fb1e00dcb4af6289521c Mon Sep 17 00:00:00 2001 From: Iyad Kandalaft Date: Sat, 26 Mar 2016 00:17:23 +0100 Subject: [PATCH 01/18] initial files by IyadKandalaft --- config/datatypes_conf.xml.sample | 58 + .../ref_to_seq_taxonomy_converter.py | 31 + .../ref_to_seq_taxonomy_converter.xml | 12 + lib/galaxy/datatypes/mothur.py | 1171 +++++++++++++++++ 4 files changed, 1272 insertions(+) create mode 100644 lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py create mode 100644 lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml create mode 100644 lib/galaxy/datatypes/mothur.py diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index f321bb5b59d..fccb654fbf5 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -490,6 +490,45 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py new file mode 100644 index 00000000000..38572b979d0 --- /dev/null +++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py @@ -0,0 +1,31 @@ +#!/usr/bin/env python +""" +convert a ref.taxonommy file to a seq.taxonomy file +Usage: +%python ref_to_seq_taxonomy_converter.py +""" + +import sys, os, re +from math import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err( msg ): + sys.stderr.write( "%s" % msg ) + sys.exit() + +def __main__(): + infile_name = sys.argv[1] + outfile = open( sys.argv[2], 'w' ) + pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)]))*(;)?)$' + for i, line in enumerate( file( infile_name ) ): + line = line.rstrip() # eliminate trailing space and new line characters + if not line or line.startswith( '#' ): + continue + fields = line.split('\t') + # make sure the 2nd field (taxonomy) ends with a ; + outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$','',fields[1]))) + + outfile.close() + +if __name__ == "__main__": __main__() \ No newline at end of file diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml new file mode 100644 index 00000000000..83d406f8cf8 --- /dev/null +++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml @@ -0,0 +1,12 @@ + + converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format + ref_to_seq_taxonomy_converter.py $input $output + + + + + + + + + \ No newline at end of file diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py new file mode 100644 index 00000000000..a10a470a0a0 --- /dev/null +++ b/lib/galaxy/datatypes/mothur.py @@ -0,0 +1,1171 @@ +""" +Mothur Metagenomics Datatypes +James E Johnson - University of Minnesota +Iyad Kandalaft - Agriculture and Agri-Foods Canda +""" + +import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re +import galaxy.model +from galaxy.datatypes.sniff import * +from galaxy.datatypes.metadata import MetadataElement +from galaxy.datatypes.data import Text +from galaxy.datatypes.tabular import Tabular +from galaxy.datatypes.sequence import Fasta +from galaxy import util +from galaxy.datatypes.images import Html +import pkg_resources + +log = logging.getLogger(__name__) + +## Mothur Classes + +class Otu( Text ): + file_ext = 'otu' + MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 ) + MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] ) + def __init__(self, **kwd): + Text.__init__( self, **kwd ) + def set_meta( self, dataset, overwrite = True, **kwd ): + if dataset.has_data(): + label_names = set() + ncols = 0 + data_lines = 0 + comment_lines = 0 + try: + fh = open( dataset.file_name ) + for line in fh: + fields = line.strip().split('\t') + if len(fields) >= 2: + data_lines += 1 + ncols = max(ncols,len(fields)) + label_names.add(fields[0]) + else: + comment_lines += 1 + # Set the discovered metadata values for the dataset + dataset.metadata.data_lines = data_lines + dataset.metadata.columns = ncols + dataset.metadata.labels = [] + dataset.metadata.labels += label_names + dataset.metadata.labels.sort() + finally: + fh.close() + + def sniff( self, filename ): + """ + Determines whether the file is a otu (operational taxonomic unit) format + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + if line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) < 2: + return False + try: + check = int(linePieces[1]) + if check + 2 != len(linePieces): + return False + except ValueError: + return False + count += 1 + if count == 5: + return True + fh.close() + if count < 5 and count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class Sabund( Otu ): + file_ext = 'sabund' + def __init__(self, **kwd): + """ + # http://www.mothur.org/wiki/Sabund_file + """ + Otu.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + Otu.init_meta( self, dataset, copy_from=copy_from ) + def sniff( self, filename ): + """ + Determines whether the file is a otu (operational taxonomic unit) format + labelcount[value(1..n)] + + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + if line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) < 2: + return False + try: + check = int(linePieces[1]) + if check + 2 != len(linePieces): + return False + for i in range( 2, len(linePieces)): + ival = int(linePieces[i]) + except ValueError: + return False + count += 1 + if count >= 5: + return True + fh.close() + if count < 5 and count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class GroupAbund( Otu ): + file_ext = 'grpabund' + MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + def __init__(self, **kwd): + Otu.__init__( self, **kwd ) + # self.column_names[0] = ['label'] + # self.column_names[1] = ['group'] + # self.column_names[2] = ['count'] + """ + def init_meta( self, dataset, copy_from=None ): + Otu.init_meta( self, dataset, copy_from=copy_from ) + """ + def init_meta( self, dataset, copy_from=None ): + Otu.init_meta( self, dataset, copy_from=copy_from ) + def set_meta( self, dataset, overwrite = True, skip=1, max_data_lines = 100000, **kwd ): + # See if file starts with header line + if dataset.has_data(): + label_names = set() + group_names = set() + data_lines = 0 + comment_lines = 0 + ncols = 0 + try: + fh = open( dataset.file_name ) + line = fh.readline() + fields = line.strip().split('\t') + ncols = max(ncols,len(fields)) + if fields[0] == 'label' and fields[1] == 'Group': + skip=1 + comment_lines += 1 + else: + skip=0 + data_lines += 1 + label_names.add(fields[0]) + group_names.add(fields[1]) + for line in fh: + data_lines += 1 + fields = line.strip().split('\t') + ncols = max(ncols,len(fields)) + label_names.add(fields[0]) + group_names.add(fields[1]) + # Set the discovered metadata values for the dataset + dataset.metadata.data_lines = data_lines + dataset.metadata.columns = ncols + dataset.metadata.labels = [] + dataset.metadata.labels += label_names + dataset.metadata.labels.sort() + dataset.metadata.groups = [] + dataset.metadata.groups += group_names + dataset.metadata.groups.sort() + dataset.metadata.skip = skip + finally: + fh.close() + + def sniff( self, filename, vals_are_int=False): + """ + Determines whether the file is a otu (operational taxonomic unit) Shared format + labelgroupcount[value(1..n)] + The first line is column headings as of Mothur v 1.20 + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + if line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) < 3: + return False + if count > 0 or linePieces[0] != 'label': + try: + check = int(linePieces[2]) + if check + 3 != len(linePieces): + return False + for i in range( 3, len(linePieces)): + if vals_are_int: + ival = int(linePieces[i]) + else: + fval = float(linePieces[i]) + except ValueError: + return False + count += 1 + if count >= 5: + return True + fh.close() + if count < 5 and count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class SecondaryStructureMap(Tabular): + file_ext = 'map' + def __init__(self, **kwd): + """Initialize secondary structure map datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = ['Map'] + + def sniff( self, filename ): + """ + Determines whether the file is a secondary structure map format + A single column with an integer value which indicates the row that this row maps to. + check you make sure is structMap[10] = 380 then structMap[380] = 10. + """ + try: + fh = open( filename ) + line_num = 0 + rowidxmap = {} + while True: + line = fh.readline() + line_num += 1 + line = line.strip() + if not line: + break #EOF + if line: + try: + pointer = int(line) + if pointer > 0: + if pointer > line_num: + rowidxmap[line_num] = pointer + elif pointer < line_num & rowidxmap[pointer] != line_num: + return False + except ValueError: + return False + fh.close() + if count < 5 and count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class SequenceAlignment( Fasta ): + file_ext = 'align' + def __init__(self, **kwd): + Fasta.__init__( self, **kwd ) + """Initialize AlignCheck datatype""" + + def sniff( self, filename ): + """ + Determines whether the file is in Mothur align fasta format + Each sequence line must be the same length + """ + + try: + fh = open( filename ) + len = -1 + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: #first non-empty line + if line.startswith( '>' ): + #The next line.strip() must not be '', nor startwith '>' + line = fh.readline().strip() + if line == '' or line.startswith( '>' ): + break + if len < 0: + len = len(line) + elif len != len(line): + return False + else: + break #we found a non-empty line, but its not a fasta header + if len > 0: + return True + except: + pass + finally: + fh.close() + return False + +class AlignCheck( Tabular ): + file_ext = 'align.check' + def __init__(self, **kwd): + """Initialize AlignCheck datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] + self.column_types = ['str','int','int','int','int','int','int','int'] + self.comment_lines = 1 + + def set_meta( self, dataset, overwrite = True, **kwd ): + # Tabular.set_meta( self, dataset, overwrite = overwrite, first_line_is_header = True, skip = 1 ) + data_lines = 0 + if dataset.has_data(): + dataset_fh = open( dataset.file_name ) + while True: + line = dataset_fh.readline() + if not line: break + data_lines += 1 + dataset_fh.close() + dataset.metadata.comment_lines = 1 + dataset.metadata.data_lines = data_lines - 1 if data_lines > 0 else 0 + dataset.metadata.column_names = self.column_names + dataset.metadata.column_types = self.column_types + +class AlignReport(Tabular): + """ +QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template +AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6 + """ + file_ext = 'align.report' + def __init__(self, **kwd): + """Initialize AlignCheck datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = ['QueryName','QueryLength','TemplateName','TemplateLength','SearchMethod','SearchScore', + 'AlignmentMethod','QueryStart','QueryEnd','TemplateStart','TemplateEnd', + 'PairwiseAlignmentLength','GapsInQuery','GapsInTemplate','LongestInsert','SimBtwnQuery&Template' + ] + +class BellerophonChimera( Tabular ): + file_ext = 'bellerophon.chimera' + def __init__(self, **kwd): + """Initialize AlignCheck datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = ['Name','Score','Left','Right'] + +class SecondaryStructureMatch(Tabular): + """ + name pound dash plus equal loop tilde total + 9_1_12 42 68 8 28 275 420 872 + 9_1_14 36 68 6 26 266 422 851 + 9_1_15 44 68 8 28 276 418 873 + 9_1_16 34 72 6 30 267 430 860 + 9_1_18 46 80 2 36 261 + """ + def __init__(self, **kwd): + """Initialize SecondaryStructureMatch datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] + +class DistanceMatrix( Text ): + file_ext = 'dist' + """Add metadata elements""" + MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?' ) + + def init_meta( self, dataset, copy_from=None ): + Text.init_meta( self, dataset, copy_from=copy_from ) + + def set_meta( self, dataset, overwrite = True, skip = 0, **kwd ): + Text.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) + try: + fh = open( dataset.file_name ) + line = fh.readline().strip().strip() + dataset.metadata.sequence_count = int(line) + except Exception, e: + log.warn("DistanceMatrix set_meta %s" % e) + finally: + fh.close() + +class LowerTriangleDistanceMatrix(DistanceMatrix): + file_ext = 'lower.dist' + def __init__(self, **kwd): + """Initialize secondary structure map datatype""" + DistanceMatrix.__init__( self, **kwd ) + + def init_meta( self, dataset, copy_from=None ): + DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) + + def sniff( self, filename ): + """ + Determines whether the file is a lower-triangle distance matrix (phylip) format + The first line has the number of sequences in the matrix. + The remaining lines have the sequence name followed by a list of distances from all preceeding sequences + 5 + U68589 + U68590 0.3371 + U68591 0.3609 0.3782 + U68592 0.4155 0.3197 0.4148 + U68593 0.2872 0.1690 0.3361 0.2842 + """ + try: + fh = open( filename ) + count = 0 + line = fh.readline() + sequence_count = int(line.strip()) + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + # Split into fields + linePieces = line.split('\t') + # Each line should have the same number of + # fields as the Python line index + linePieces = line.split('\t') + if len(linePieces) != (count + 1): + return False + # Distances should be floats + try: + for linePiece in linePieces[2:]: + check = float(linePiece) + except ValueError: + return False + # Increment line counter + count += 1 + # Only check first 5 lines + if count == 5: + return True + fh.close() + if count < 5 and count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class SquareDistanceMatrix(DistanceMatrix): + file_ext = 'square.dist' + + def __init__(self, **kwd): + DistanceMatrix.__init__( self, **kwd ) + def init_meta( self, dataset, copy_from=None ): + DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) + + def sniff( self, filename ): + """ + Determines whether the file is a square distance matrix (Column-formatted distance matrix) format + The first line has the number of sequences in the matrix. + The following lines have the sequence name in the first column plus a column for the distance to each sequence + in the row order in which they appear in the matrix. + 3 + U68589 0.0000 0.3371 0.3610 + U68590 0.3371 0.0000 0.3783 + U68590 0.3371 0.0000 0.3783 + """ + try: + fh = open( filename ) + count = 0 + line = fh.readline() + line = line.strip() + sequence_count = int(line) + col_cnt = seq_cnt + 1 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + if line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) != col_cnt : + return False + try: + for i in range(1, col_cnt): + check = float(linePieces[i]) + except ValueError: + return False + count += 1 + if count == 5: + return True + fh.close() + if count < 5 and count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class PairwiseDistanceMatrix(DistanceMatrix,Tabular): + file_ext = 'pair.dist' + def __init__(self, **kwd): + """Initialize secondary structure map datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = ['Sequence','Sequence','Distance'] + self.column_types = ['str','str','float'] + def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): + Tabular.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) + + def sniff( self, filename ): + """ + Determines whether the file is a pairwise distance matrix (Column-formatted distance matrix) format + The first and second columns have the sequence names and the third column is the distance between those sequences. + """ + try: + fh = open( filename ) + count = 0 + all_ints = True + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + if line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) != 3: + return False + try: + check = float(linePieces[2]) + try: + # See if it's also an integer + check_int = int(linePieces[2]) + except ValueError: + # At least one value is not an + # integer + all_ints = False + except ValueError: + return False + count += 1 + if count == 5: + if not all_ints: + return True + else: + return False + fh.close() + if count < 5 and count > 0: + if not all_ints: + return True + else: + return False + except: + pass + finally: + fh.close() + return False + +class AlignCheck(Tabular): + file_ext = 'align.check' + def __init__(self, **kwd): + """Initialize secondary structure map datatype""" + Tabular.__init__( self, **kwd ) + self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] + self.columns = 8 + +class Names(Tabular): + file_ext = 'names' + def __init__(self, **kwd): + """ + # http://www.mothur.org/wiki/Name_file + Name file shows the relationship between a representative sequence(col 1) and the sequences(comma-separated) it represents(col 2) + """ + Tabular.__init__( self, **kwd ) + self.column_names = ['name','representatives'] + self.columns = 2 + +class Summary(Tabular): + file_ext = 'summary' + def __init__(self, **kwd): + """summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file""" + Tabular.__init__( self, **kwd ) + self.column_names = ['seqname','start','end','nbases','ambigs','polymer'] + self.columns = 6 + +class Group(Tabular): + file_ext = 'groups' + MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + def __init__(self, **kwd): + """ + # http://www.mothur.org/wiki/Groups_file + Group file assigns sequence (col 1) to a group (col 2) + """ + Tabular.__init__( self, **kwd ) + self.column_names = ['name','group'] + self.columns = 2 + def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): + Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) + group_names = set() + try: + fh = open( dataset.file_name ) + for line in fh: + fields = line.strip().split('\t') + try: + group_names.add(fields[1]) + except IndexError: + # Ignore missing 2nd column + pass + dataset.metadata.groups = [] + dataset.metadata.groups += group_names + finally: + fh.close() + +class AccNos(Tabular): + file_ext = 'accnos' + def __init__(self, **kwd): + """A list of names""" + Tabular.__init__( self, **kwd ) + self.column_names = ['name'] + self.columns = 1 + +class Oligos( Text ): + file_ext = 'oligos' + + def sniff( self, filename ): + """ + # http://www.mothur.org/wiki/Oligos_File + Determines whether the file is a otu (operational taxonomic unit) format + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + else: + if line[0] != '#': + linePieces = line.split('\t') + if len(linePieces) == 2 and re.match('forward|reverse',linePieces[0]): + count += 1 + continue + elif len(linePieces) == 3 and re.match('barcode',linePieces[0]): + count += 1 + continue + else: + return False + if count > 20: + return True + if count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class Frequency(Tabular): + file_ext = 'freq' + def __init__(self, **kwd): + """A list of names""" + Tabular.__init__( self, **kwd ) + self.column_names = ['position','frequency'] + self.column_types = ['int','float'] + + def sniff( self, filename ): + """ + Determines whether the file is a frequency tabular format for chimera analysis + #1.14.0 + 0 0.000 + 1 0.000 + ... + 155 0.975 + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + else: + if line[0] != '#': + try: + linePieces = line.split('\t') + i = int(linePieces[0]) + f = float(linePieces[1]) + count += 1 + continue + except: + return False + if count > 20: + return True + if count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class Quantile(Tabular): + file_ext = 'quan' + MetadataElement( name="filtered", default=False, no_value=False, optional=True , desc="Quantiles calculated using a mask", readonly=True) + MetadataElement( name="masked", default=False, no_value=False, optional=True , desc="Quantiles calculated using a frequency filter", readonly=True) + def __init__(self, **kwd): + """Quantiles for chimera analysis""" + Tabular.__init__( self, **kwd ) + self.column_names = ['num','ten','twentyfive','fifty','seventyfive','ninetyfive','ninetynine'] + self.column_types = ['int','float','float','float','float','float','float'] + def sniff( self, filename ): + """ + Determines whether the file is a quantiles tabular format for chimera analysis + 1 0 0 0 0 0 0 + 2 0.309198 0.309198 0.37161 0.37161 0.37161 0.37161 + 3 0.510982 0.563213 0.693529 0.858939 1.07442 1.20608 + ... + """ + try: + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + else: + if line[0] != '#': + try: + linePieces = line.split('\t') + i = int(linePieces[0]) + f = float(linePieces[1]) + f = float(linePieces[2]) + f = float(linePieces[3]) + f = float(linePieces[4]) + f = float(linePieces[5]) + f = float(linePieces[6]) + count += 1 + continue + except: + return False + if count > 10: + return True + if count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class LaneMask(Text): + file_ext = 'filter' + + def sniff( self, filename ): + """ + Determines whether the file is a lane mask filter: 1 line consisting of zeros and ones. + """ + try: + fh = open( filename ) + while True: + buff = fh.read(1000) + if not buff: + break #EOF + else: + if not re.match('^[01]+$',line): + return False + return True + except: + pass + finally: + close(fh) + return False + +class CountTable(Tabular): + MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + file_ext = 'count_table' + + def __init__(self, **kwd): + """ + # http://www.mothur.org/wiki/Count_File + A table with first column names and following columns integer counts + # Example 1: + Representative_Sequence total + U68630 1 + U68595 1 + U68600 1 + # Example 2 (with group columns): + Representative_Sequence total forest pasture + U68630 1 1 0 + U68595 1 1 0 + U68600 1 1 0 + U68591 1 1 0 + U68647 1 0 1 + """ + Tabular.__init__( self, **kwd ) + self.column_names = ['name','total'] + + def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): + try: + data_lines = 0; + fh = open( dataset.file_name ) + line = fh.readline() + if line: + line = line.strip() + colnames = line.split() + if len(colnames) > 1: + dataset.metadata.columns = len( colnames ) + if len(colnames) > 2: + dataset.metadata.groups = colnames[2:] + column_types = ['str'] + for i in range(1,len(colnames)): + column_types.append('int') + dataset.metadata.column_types = column_types + dataset.metadata.comment_lines = 1 + while line: + line = fh.readline() + if not line: break + data_lines += 1 + dataset.metadata.data_lines = data_lines + finally: + close(fh) + +class RefTaxonomy(Tabular): + file_ext = 'ref.taxonomy' + """ + # http://www.mothur.org/wiki/Taxonomy_outline + A table with 2 or 3 columns: + - SequenceName + - Taxonomy (semicolon-separated taxonomy in descending order) + - integer ? + Example: 2-column ( http://www.mothur.org/wiki/Taxonomy_outline ) + X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; + X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; + AF052717.1 Eukaryota;Parabasalidea; + Example: 3-column ( http://vamps.mbl.edu/resources/databases.php ) + v3_AA008 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus 5 + v3_AA016 Bacteria 120 + v3_AA019 Archaea;Crenarchaeota;Marine_Group_I 1 + """ + def __init__(self, **kwd): + Tabular.__init__( self, **kwd ) + self.column_names = ['name','taxonomy'] + + def sniff( self, filename ): + """ + Determines whether the file is a Reference Taxonomy + """ + try: + pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$' + fh = open( filename ) + count = 0 + # VAMPS taxonomy files do not require a semicolon after the last taxonomy category + # but assume assume the file will have some multi-level taxonomy assignments + found_semicolons = False + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: + fields = line.split('\t') + if not (2 <= len(fields) <= 3): + return False + if not re.match(pat,fields[1]): + return False + if not found_semicolons and str(fields[1]).count(';') > 0: + found_semicolons = True + if len(fields) == 3: + check = int(fields[2]) + count += 1 + if count > 100: + break + if count > 0: + # This will be true if at least one entry + # has semicolons in the 2nd column + return found_semicolons + except: + pass + finally: + fh.close() + return False + +class SequenceTaxonomy(RefTaxonomy): + file_ext = 'seq.taxonomy' + """ + # http://www.mothur.org/wiki/Taxonomy_outline + A table with 2 columns: + - SequenceName + - Taxonomy (semicolon-separated taxonomy in descending order) + Example: + X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; + X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; + AF052717.1 Eukaryota;Parabasalidea; + """ + def __init__(self, **kwd): + Tabular.__init__( self, **kwd ) + self.column_names = ['name','taxonomy'] + + def sniff( self, filename ): + """ + Determines whether the file is a SequenceTaxonomy + """ + try: + pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;])+$' + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: + fields = line.split('\t') + if len(fields) != 2: + return False + if not re.match(pat,fields[1]): + return False + count += 1 + if count > 10: + break + if count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class RDPSequenceTaxonomy(SequenceTaxonomy): + file_ext = 'rdp.taxonomy' + """ + A table with 2 columns: + - SequenceName + - Taxonomy (semicolon-separated taxonomy in descending order, RDP requires exactly 6 levels deep) + Example: + AB001518.1 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;unclassified_Sphingobacteriales; + AB001724.1 Bacteria;Cyanobacteria;Cyanobacteria;Family_II;GpIIa; + AB001774.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; + """ + def sniff( self, filename ): + """ + Determines whether the file is a SequenceTaxonomy + """ + try: + pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;]){6}$' + fh = open( filename ) + count = 0 + while True: + line = fh.readline() + if not line: + break #EOF + line = line.strip() + if line: + fields = line.split('\t') + if len(fields) != 2: + return False + if not re.match(pat,fields[1]): + return False + count += 1 + if count > 10: + break + if count > 0: + return True + except: + pass + finally: + fh.close() + return False + +class ConsensusTaxonomy(Tabular): + file_ext = 'cons.taxonomy' + def __init__(self, **kwd): + """A list of names""" + Tabular.__init__( self, **kwd ) + self.column_names = ['OTU','count','taxonomy'] + +class TaxonomySummary(Tabular): + file_ext = 'tax.summary' + def __init__(self, **kwd): + """A Summary of taxon classification""" + Tabular.__init__( self, **kwd ) + self.column_names = ['taxlevel','rankID','taxon','daughterlevels','total'] + +class Phylip(Text): + file_ext = 'phy' + + def sniff( self, filename ): + """ + Determines whether the file is in Phylip format (Interleaved or Sequential) + The first line of the input file contains the number of species and the + number of characters, in free format, separated by blanks (not by + commas). The information for each species follows, starting with a + ten-character species name (which can include punctuation marks and blanks), + and continuing with the characters for that species. + http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles + Interleaved Example: + 6 39 + Archaeopt CGATGCTTAC CGCCGATGCT + HesperorniCGTTACTCGT TGTCGTTACT + BaluchitheTAATGTTAAT TGTTAATGTT + B. virginiTAATGTTCGT TGTTAATGTT + BrontosaurCAAAACCCAT CATCAAAACC + B.subtilisGGCAGCCAAT CACGGCAGCC + + TACCGCCGAT GCTTACCGC + CGTTGTCGTT ACTCGTTGT + AATTGTTAAT GTTAATTGT + CGTTGTTAAT GTTCGTTGT + CATCATCAAA ACCCATCAT + AATCACGGCA GCCAATCAC + """ + try: + fh = open( filename ) + # counts line + line = fh.readline().strip() + linePieces = line.split() + count = int(linePieces[0]) + seq_len = int(linePieces[1]) + # data lines + """ + TODO check data lines + while True: + line = fh.readline() + # name is the first 10 characters + name = line[0:10] + seq = line[10:].strip() + # nucleic base or amino acid 1-char designators (spaces allowed) + bases = ''.join(seq.split()) + # float per base (each separated by space) + """ + return True + except: + pass + finally: + close(fh) + return False + + +class Axes(Tabular): + file_ext = 'axes' + + def __init__(self, **kwd): + """Initialize axes datatype""" + Tabular.__init__( self, **kwd ) + def sniff( self, filename ): + """ + Determines whether the file is an axes format + The first line may have column headings. + The following lines have the name in the first column plus float columns for each axis. + ==> 98_sq_phylip_amazon.fn.unique.pca.axes <== + group axis1 axis2 + forest 0.000000 0.145743 + pasture 0.145743 0.000000 + + ==> 98_sq_phylip_amazon.nmds.axes <== + axis1 axis2 + U68589 0.262608 -0.077498 + U68590 0.027118 0.195197 + U68591 0.329854 0.014395 + """ + try: + fh = open( filename ) + count = 0 + line = fh.readline() + line = line.strip() + col_cnt = None + all_integers = True + while True: + line = fh.readline() + line = line.strip() + if not line: + break #EOF + if line: + fields = line.split('\t') + if col_cnt == None: # ignore values in first line as they may be column headings + col_cnt = len(fields) + # There should be at least 2 columns + if col_cnt < 2: + return False + else: + if len(fields) != col_cnt : + return False + try: + for i in range(1, col_cnt): + check = float(fields[i]) + # Check abs value is <= 1.0 + if abs(check) > 1.0: + return False + # Also test for whether value is an integer + try: + check = int(fields[i]) + except ValueError: + all_integers = False + except ValueError: + return False + count += 1 + if count > 10: + break + if count > 0: + if not all_integers: + # At least one value was a float + return True + else: + return False + except: + pass + finally: + fh.close() + return False + +class SffFlow(Tabular): + MetadataElement( name="flow_values", default="", no_value="", optional=True , desc="Total number of flow values", readonly=True) + MetadataElement( name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False) + file_ext = 'sff.flow' + """ + # http://www.mothur.org/wiki/Flow_file + The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400. + Following lines contain: + - SequenceName + - the number of useable flows as defined by 454's software + - the flow intensity for each base going in the order of TACG. + Example: + 800 + GQY1XT001CQL4K 85 1.04 0.00 1.00 0.02 0.03 1.02 0.05 ... + GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 ... + GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ... + """ + def __init__(self, **kwd): + Tabular.__init__( self, **kwd ) + + def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): + Tabular.set_meta(self, dataset, overwrite, 1, max_data_lines) + try: + fh = open( dataset.file_name ) + line = fh.readline() + line = line.strip() + flow_values = int(line) + dataset.metadata.flow_values = flow_values + finally: + fh.close() + + def make_html_table( self, dataset, skipchars=[] ): + """Create HTML table, used for displaying peek""" + out = [''] + comments = [] + try: + # Generate column header + out.append('') + out.append( '' % 1 ) + out.append( '' % 2 ) + for i in range( 3, dataset.metadata.columns+1 ): + base = dataset.metadata.flow_order[(i+1)%4] + out.append( '' % (i-2,base) ) + out.append('') + out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) + out.append( '
%d. Name%d. Flows%d. %d %s
' ) + out = "".join( out ) + except Exception, exc: + out = "Can't create peek %s" % str( exc ) + return out + +if __name__ == '__main__': + import doctest, sys + doctest.testmod(sys.modules[__name__]) From f8a2dbd05a87782f5f0c30540ef463330d040589 Mon Sep 17 00:00:00 2001 From: shiltemann Date: Sat, 26 Mar 2016 00:32:55 +0100 Subject: [PATCH 02/18] add mothur prefix --- config/datatypes_conf.xml.sample | 74 +++++++++---------- .../ref_to_seq_taxonomy_converter.xml | 6 +- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index fccb654fbf5..8deeae308fa 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -491,44 +491,44 @@ - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + - + - - + - - diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index 6da66b6eb45..39092eb6262 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -20,7 +20,7 @@ log = logging.getLogger(__name__) ## Mothur Classes class Otu( Text ): - file_ext = 'otu' + file_ext = 'mothur.otu' MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 ) MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] ) def __init__(self, **kwd): @@ -61,20 +61,20 @@ class Otu( Text ): line = line.strip() if not line: break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 2: - return False + if line and line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) < 2: + return False + if count >= 1: try: check = int(linePieces[1]) if check + 2 != len(linePieces): return False except ValueError: return False - count += 1 - if count == 5: - return True + count += 1 + if count == 5: + return True if count < 5 and count > 0: return True except: @@ -82,7 +82,7 @@ class Otu( Text ): return False class Sabund( Otu ): - file_ext = 'sabund' + file_ext = 'mothur.sabund' def __init__(self, **kwd): """ # http://www.mothur.org/wiki/Sabund_file @@ -104,30 +104,27 @@ class Sabund( Otu ): line = line.strip() if not line: break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 2: + if line and line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) < 2: + return False + try: + check = int(linePieces[1]) + if check + 2 != len(linePieces): return False - try: - check = int(linePieces[1]) - if check + 2 != len(linePieces): - return False - for i in range( 2, len(linePieces)): - ival = int(linePieces[i]) - except ValueError: - return False - count += 1 - if count >= 5: - return True - if count < 5 and count > 0: + for i in range( 2, len(linePieces)): + ival = int(linePieces[i]) + except ValueError: + return False + count += 1 + if count > 0: return True except: pass return False class GroupAbund( Otu ): - file_ext = 'grpabund' + file_ext = 'mothur.shared' MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) def __init__(self, **kwd): Otu.__init__( self, **kwd ) @@ -192,26 +189,25 @@ class GroupAbund( Otu ): line = line.strip() if not line: break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 3: - return False - if count > 0 or linePieces[0] != 'label': - try: - check = int(linePieces[2]) - if check + 3 != len(linePieces): - return False - for i in range( 3, len(linePieces)): - if vals_are_int: - ival = int(linePieces[i]) - else: - fval = float(linePieces[i]) - except ValueError: + if line and line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) < 3: + return False + if count > 0 or linePieces[0] != 'label': + try: + check = int(linePieces[2]) + if check + 3 != len(linePieces): return False - count += 1 - if count >= 5: - return True + for i in range( 3, len(linePieces)): + if vals_are_int: + ival = int(linePieces[i]) + else: + fval = float(linePieces[i]) + except ValueError: + return False + count += 1 + if count >= 5: + return True if count < 5 and count > 0: return True except: @@ -219,7 +215,7 @@ class GroupAbund( Otu ): return False class SecondaryStructureMap(Tabular): - file_ext = 'map' + file_ext = 'mothur.map' def __init__(self, **kwd): """Initialize secondary structure map datatype""" Tabular.__init__( self, **kwd ) @@ -244,21 +240,21 @@ class SecondaryStructureMap(Tabular): if line: try: pointer = int(line) - if pointer > 0: - if pointer > line_num: - rowidxmap[line_num] = pointer - elif pointer < line_num & rowidxmap[pointer] != line_num: + if pointer > line_num: + rowidxmap[pointer] = line_num + elif pointer > 0 or line_num in rowidxmap: + if rowidxmap[line_num] != pointer: return False except ValueError: return False - if count < 5 and count > 0: - return True except: - pass - return False + return False + if line_num < 3: + return False + return True class SequenceAlignment( Fasta ): - file_ext = 'align' + file_ext = 'mothur.align' def __init__(self, **kwd): Fasta.__init__( self, **kwd ) """Initialize AlignCheck datatype""" @@ -296,7 +292,7 @@ class SequenceAlignment( Fasta ): return False class AlignCheck( Tabular ): - file_ext = 'align.check' + file_ext = 'mothur.align.check' def __init__(self, **kwd): """Initialize AlignCheck datatype""" Tabular.__init__( self, **kwd ) @@ -324,7 +320,7 @@ class AlignReport(Tabular): QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6 """ - file_ext = 'align.report' + file_ext = 'mothur.align.report' def __init__(self, **kwd): """Initialize AlignCheck datatype""" Tabular.__init__( self, **kwd ) @@ -334,7 +330,7 @@ AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 ] class BellerophonChimera( Tabular ): - file_ext = 'bellerophon.chimera' + file_ext = 'mothur.bellerophon.chimera' def __init__(self, **kwd): """Initialize AlignCheck datatype""" Tabular.__init__( self, **kwd ) @@ -355,7 +351,7 @@ class SecondaryStructureMatch(Tabular): self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] class DistanceMatrix( Text ): - file_ext = 'dist' + file_ext = 'mothur.dist' """Add metadata elements""" MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?' ) @@ -366,13 +362,15 @@ class DistanceMatrix( Text ): Text.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) try: with open( dataset.file_name ) as fh: - line = fh.readline().strip().strip() + line = '@' + while line[0] == '@': + line = fh.readline().strip().strip() dataset.metadata.sequence_count = int(line) except Exception, e: log.warn("DistanceMatrix set_meta %s" % e) class LowerTriangleDistanceMatrix(DistanceMatrix): - file_ext = 'lower.dist' + file_ext = 'mothur.lower.dist' def __init__(self, **kwd): """Initialize secondary structure map datatype""" DistanceMatrix.__init__( self, **kwd ) @@ -428,7 +426,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix): return False class SquareDistanceMatrix(DistanceMatrix): - file_ext = 'square.dist' + file_ext = 'mothur.square.dist' def __init__(self, **kwd): DistanceMatrix.__init__( self, **kwd ) @@ -449,17 +447,15 @@ class SquareDistanceMatrix(DistanceMatrix): try: with open( filename ) as fh: count = 0 - line = fh.readline() - line = line.strip() - seq_cnt = int(line) - col_cnt = seq_cnt + 1 while True: - line = fh.readline() - line = line.strip() + line = fh.readline().strip() if not line: break #EOF - if line: - if line[0] != '@': + if line[0] != '@': + if count == 0: + seq_cnt = int(line) + col_cnt = seq_cnt + 1 + else: linePieces = line.split('\t') if len(linePieces) != col_cnt : return False @@ -468,17 +464,15 @@ class SquareDistanceMatrix(DistanceMatrix): check = float(linePieces[i]) except ValueError: return False - count += 1 - if count == 5: - return True - if count < 5 and count > 0: + count += 1 + if count > 2: return True except: pass return False class PairwiseDistanceMatrix(DistanceMatrix,Tabular): - file_ext = 'pair.dist' + file_ext = 'mothur.pair.dist' def __init__(self, **kwd): """Initialize secondary structure map datatype""" Tabular.__init__( self, **kwd ) @@ -501,28 +495,27 @@ class PairwiseDistanceMatrix(DistanceMatrix,Tabular): line = line.strip() if not line: break #EOF - if line: - if line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) != 3: - return False + if line and line[0] != '@': + linePieces = line.split('\t') + if len(linePieces) != 3: + return False + try: + check = float(linePieces[2]) try: - check = float(linePieces[2]) - try: - # See if it's also an integer - check_int = int(linePieces[2]) - except ValueError: - # At least one value is not an - # integer - all_ints = False + # See if it's also an integer + check_int = int(linePieces[2]) except ValueError: + # At least one value is not an + # integer + all_ints = False + except ValueError: + return False + count += 1 + if count == 5: + if not all_ints: + return True + else: return False - count += 1 - if count == 5: - if not all_ints: - return True - else: - return False if count < 5 and count > 0: if not all_ints: return True @@ -532,16 +525,9 @@ class PairwiseDistanceMatrix(DistanceMatrix,Tabular): pass return False -class AlignCheck(Tabular): - file_ext = 'align.check' - def __init__(self, **kwd): - """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] - self.columns = 8 class Names(Tabular): - file_ext = 'names' + file_ext = 'mothur.names' def __init__(self, **kwd): """ # http://www.mothur.org/wiki/Name_file @@ -552,7 +538,7 @@ class Names(Tabular): self.columns = 2 class Summary(Tabular): - file_ext = 'summary' + file_ext = 'mothur.summary' def __init__(self, **kwd): """summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file""" Tabular.__init__( self, **kwd ) @@ -560,7 +546,7 @@ class Summary(Tabular): self.columns = 6 class Group(Tabular): - file_ext = 'groups' + file_ext = 'mothur.groups' MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) def __init__(self, **kwd): """ @@ -588,7 +574,7 @@ class Group(Tabular): pass class AccNos(Tabular): - file_ext = 'accnos' + file_ext = 'mothur.accnos' def __init__(self, **kwd): """A list of names""" Tabular.__init__( self, **kwd ) @@ -596,7 +582,7 @@ class AccNos(Tabular): self.columns = 1 class Oligos( Text ): - file_ext = 'oligos' + file_ext = 'mothur.oligos' def sniff( self, filename ): """ @@ -631,7 +617,7 @@ class Oligos( Text ): return False class Frequency(Tabular): - file_ext = 'freq' + file_ext = 'mothur.freq' def __init__(self, **kwd): """A list of names""" Tabular.__init__( self, **kwd ) @@ -656,17 +642,18 @@ class Frequency(Tabular): if not line: break #EOF else: + if count == 0 and line[0] != '#': + return False if line[0] != '#': + linePieces = line.split('\t') + if len(linePieces) != 2: + return False try: - linePieces = line.split('\t') i = int(linePieces[0]) f = float(linePieces[1]) - count += 1 - continue except: return False - if count > 20: - return True + count += 1 if count > 0: return True except: @@ -674,7 +661,7 @@ class Frequency(Tabular): return False class Quantile(Tabular): - file_ext = 'quan' + file_ext = 'mothur.quan' MetadataElement( name="filtered", default=False, no_value=False, optional=True , desc="Quantiles calculated using a mask", readonly=True) MetadataElement( name="masked", default=False, no_value=False, optional=True , desc="Quantiles calculated using a frequency filter", readonly=True) def __init__(self, **kwd): @@ -722,7 +709,7 @@ class Quantile(Tabular): return False class LaneMask(Text): - file_ext = 'filter' + file_ext = 'mothur.filter' def sniff( self, filename ): """ @@ -730,13 +717,17 @@ class LaneMask(Text): """ try: with open( filename ) as fh: + count=0 while True: - buff = fh.read(1000) - if not buff: + line = fh.readline().strip() + if not line: break #EOF else: + count+=1 if not re.match('^[01]+$',line): return False + if count != 1: + return False return True except: pass @@ -744,7 +735,7 @@ class LaneMask(Text): class CountTable(Tabular): MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) - file_ext = 'count_table' + file_ext = 'mothur.count_table' def __init__(self, **kwd): """ @@ -792,7 +783,7 @@ class CountTable(Tabular): pass class RefTaxonomy(Tabular): - file_ext = 'ref.taxonomy' + file_ext = 'mothur.ref.taxonomy' """ # http://www.mothur.org/wiki/Taxonomy_outline A table with 2 or 3 columns: @@ -849,105 +840,22 @@ class RefTaxonomy(Tabular): pass return False -class SequenceTaxonomy(RefTaxonomy): - file_ext = 'seq.taxonomy' - """ - # http://www.mothur.org/wiki/Taxonomy_outline - A table with 2 columns: - - SequenceName - - Taxonomy (semicolon-separated taxonomy in descending order) - Example: - X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; - X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; - AF052717.1 Eukaryota;Parabasalidea; - """ - def __init__(self, **kwd): - Tabular.__init__( self, **kwd ) - self.column_names = ['name','taxonomy'] - - def sniff( self, filename ): - """ - Determines whether the file is a SequenceTaxonomy - """ - try: - pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;])+$' - with open( filename ) as fh: - count = 0 - while True: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: - fields = line.split('\t') - if len(fields) != 2: - return False - if not re.match(pat,fields[1]): - return False - count += 1 - if count > 10: - break - if count > 0: - return True - except: - pass - return False - -class RDPSequenceTaxonomy(SequenceTaxonomy): - file_ext = 'rdp.taxonomy' - """ - A table with 2 columns: - - SequenceName - - Taxonomy (semicolon-separated taxonomy in descending order, RDP requires exactly 6 levels deep) - Example: - AB001518.1 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;unclassified_Sphingobacteriales; - AB001724.1 Bacteria;Cyanobacteria;Cyanobacteria;Family_II;GpIIa; - AB001774.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; - """ - def sniff( self, filename ): - """ - Determines whether the file is a SequenceTaxonomy - """ - try: - pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;]){6}$' - with open( filename ) as fh: - count = 0 - while True: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: - fields = line.split('\t') - if len(fields) != 2: - return False - if not re.match(pat,fields[1]): - return False - count += 1 - if count > 10: - break - if count > 0: - return True - except: - pass - return False - class ConsensusTaxonomy(Tabular): - file_ext = 'cons.taxonomy' + file_ext = 'mothur.cons.taxonomy' def __init__(self, **kwd): """A list of names""" Tabular.__init__( self, **kwd ) self.column_names = ['OTU','count','taxonomy'] class TaxonomySummary(Tabular): - file_ext = 'tax.summary' + file_ext = 'mothur.tax.summary' def __init__(self, **kwd): """A Summary of taxon classification""" Tabular.__init__( self, **kwd ) self.column_names = ['taxlevel','rankID','taxon','daughterlevels','total'] class Phylip(Text): - file_ext = 'phy' + file_ext = 'mothur.phy' def sniff( self, filename ): """ @@ -1000,7 +908,7 @@ class Phylip(Text): class Axes(Tabular): - file_ext = 'axes' + file_ext = 'mothur.axes' def __init__(self, **kwd): """Initialize axes datatype""" @@ -1072,7 +980,7 @@ class Axes(Tabular): class SffFlow(Tabular): MetadataElement( name="flow_values", default="", no_value="", optional=True , desc="Total number of flow values", readonly=True) MetadataElement( name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False) - file_ext = 'sff.flow' + file_ext = 'mothur.sff.flow' """ # http://www.mothur.org/wiki/Flow_file The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400. From ef32ee15fd9ee7a61c018a7e22a3cae0cc498b87 Mon Sep 17 00:00:00 2001 From: shiltemann Date: Wed, 30 Mar 2016 14:37:05 +0200 Subject: [PATCH 07/18] remove phylip datatype (not specific to mothur) --- config/datatypes_conf.xml.sample | 1 - lib/galaxy/datatypes/mothur.py | 53 -------------------------------- 2 files changed, 54 deletions(-) diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index 15122ea4417..1b487f4a984 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -550,7 +550,6 @@ - diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index 39092eb6262..1a70dd9e11f 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -854,59 +854,6 @@ class TaxonomySummary(Tabular): Tabular.__init__( self, **kwd ) self.column_names = ['taxlevel','rankID','taxon','daughterlevels','total'] -class Phylip(Text): - file_ext = 'mothur.phy' - - def sniff( self, filename ): - """ - Determines whether the file is in Phylip format (Interleaved or Sequential) - The first line of the input file contains the number of species and the - number of characters, in free format, separated by blanks (not by - commas). The information for each species follows, starting with a - ten-character species name (which can include punctuation marks and blanks), - and continuing with the characters for that species. - http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles - Interleaved Example: - 6 39 - Archaeopt CGATGCTTAC CGCCGATGCT - HesperorniCGTTACTCGT TGTCGTTACT - BaluchitheTAATGTTAAT TGTTAATGTT - B. virginiTAATGTTCGT TGTTAATGTT - BrontosaurCAAAACCCAT CATCAAAACC - B.subtilisGGCAGCCAAT CACGGCAGCC - - TACCGCCGAT GCTTACCGC - CGTTGTCGTT ACTCGTTGT - AATTGTTAAT GTTAATTGT - CGTTGTTAAT GTTCGTTGT - CATCATCAAA ACCCATCAT - AATCACGGCA GCCAATCAC - """ - try: - with open( filename ) as fh: - # counts line - line = fh.readline().strip() - linePieces = line.split() - count = int(linePieces[0]) - seq_len = int(linePieces[1]) - # data lines - """ - TODO check data lines - while True: - line = fh.readline() - # name is the first 10 characters - name = line[0:10] - seq = line[10:].strip() - # nucleic base or amino acid 1-char designators (spaces allowed) - bases = ''.join(seq.split()) - # float per base (each separated by space) - """ - return True - except: - pass - return False - - class Axes(Tabular): file_ext = 'mothur.axes' From 6ac7ec56032e25e9f883421d5aba6d1e6165e2cc Mon Sep 17 00:00:00 2001 From: shiltemann Date: Wed, 30 Mar 2016 15:13:30 +0200 Subject: [PATCH 08/18] make sniffers for otu and distmatrices stricter --- lib/galaxy/datatypes/mothur.py | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index 1a70dd9e11f..aefb87238a4 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -73,9 +73,7 @@ class Otu( Text ): except ValueError: return False count += 1 - if count == 5: - return True - if count < 5 and count > 0: + if count > 2: return True except: pass @@ -416,10 +414,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix): return False # Increment line counter count += 1 - # Only check first 5 lines - if count == 5: - return True - if count < 5 and count > 0: + if count > 2: return True except: pass @@ -511,12 +506,7 @@ class PairwiseDistanceMatrix(DistanceMatrix,Tabular): except ValueError: return False count += 1 - if count == 5: - if not all_ints: - return True - else: - return False - if count < 5 and count > 0: + if count > 2: if not all_ints: return True else: From c43235011bf211da96b4507b986850ccc59567f8 Mon Sep 17 00:00:00 2001 From: shiltemann Date: Wed, 30 Mar 2016 15:42:30 +0200 Subject: [PATCH 09/18] remove two unused classes --- lib/galaxy/datatypes/mothur.py | 21 --------------------- 1 file changed, 21 deletions(-) diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index aefb87238a4..3304138b3e0 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -327,27 +327,6 @@ AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 'PairwiseAlignmentLength','GapsInQuery','GapsInTemplate','LongestInsert','SimBtwnQuery&Template' ] -class BellerophonChimera( Tabular ): - file_ext = 'mothur.bellerophon.chimera' - def __init__(self, **kwd): - """Initialize AlignCheck datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['Name','Score','Left','Right'] - -class SecondaryStructureMatch(Tabular): - """ - name pound dash plus equal loop tilde total - 9_1_12 42 68 8 28 275 420 872 - 9_1_14 36 68 6 26 266 422 851 - 9_1_15 44 68 8 28 276 418 873 - 9_1_16 34 72 6 30 267 430 860 - 9_1_18 46 80 2 36 261 - """ - def __init__(self, **kwd): - """Initialize SecondaryStructureMatch datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] - class DistanceMatrix( Text ): file_ext = 'mothur.dist' """Add metadata elements""" From b833d385056f23dfb314e4c8162982374766e73d Mon Sep 17 00:00:00 2001 From: shiltemann Date: Wed, 30 Mar 2016 16:46:19 +0200 Subject: [PATCH 10/18] stop using deprecated 'interpreter' --- .../datatypes/converters/ref_to_seq_taxonomy_converter.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml index 1e8453de637..337d07815b6 100644 --- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml +++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml @@ -1,6 +1,6 @@ converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format - ref_to_seq_taxonomy_converter.py "$input" "$output" + python $__tool_directory__/ref_to_seq_taxonomy_converter.py "$input" "$output" From f3820538d186a1143443e47e764ad8ddc001d27f Mon Sep 17 00:00:00 2001 From: shiltemann Date: Thu, 31 Mar 2016 09:59:12 +0200 Subject: [PATCH 11/18] stylefixes --- lib/galaxy/datatypes/mothur.py | 535 ++++++++++++++++++--------------- 1 file changed, 286 insertions(+), 249 deletions(-) diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index 3304138b3e0..8b6cca7e244 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -1,66 +1,61 @@ """ Mothur Metagenomics Datatypes -James E Johnson - University of Minnesota -Iyad Kandalaft - Agriculture and Agri-Foods Canda """ - -import logging, os, os.path, sys, time, tempfile, shutil, string, glob, re -import galaxy.model -from galaxy.datatypes.sniff import * +import logging +import sys +import re from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.data import Text from galaxy.datatypes.tabular import Tabular from galaxy.datatypes.sequence import Fasta -from galaxy import util -from galaxy.datatypes.images import Html -import pkg_resources log = logging.getLogger(__name__) -## Mothur Classes -class Otu( Text ): +class Otu(Text): file_ext = 'mothur.otu' - MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 ) - MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] ) + MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0) + MetadataElement(name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[]) + def __init__(self, **kwd): - Text.__init__( self, **kwd ) - def set_meta( self, dataset, overwrite = True, **kwd ): + Text.__init__(self, **kwd) + + def set_meta(self, dataset, overwrite=True, **kwd): if dataset.has_data(): label_names = set() ncols = 0 data_lines = 0 comment_lines = 0 try: - with open( dataset.file_name ) as fh: + with open(dataset.file_name) as fh: for line in fh: fields = line.strip().split('\t') - if len(fields) >= 2: + if len(fields) >= 2: data_lines += 1 - ncols = max(ncols,len(fields)) + ncols = max(ncols, len(fields)) label_names.add(fields[0]) else: comment_lines += 1 # Set the discovered metadata values for the dataset dataset.metadata.data_lines = data_lines dataset.metadata.columns = ncols - dataset.metadata.labels = list( label_names ) + dataset.metadata.labels = list(label_names) dataset.metadata.labels.sort() except: pass - def sniff( self, filename ): + def sniff(self, filename): """ - Determines whether the file is a otu (operational taxonomic unit) format + Determines whether the file is otu (operational taxonomic unit) format """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 while True: line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF if line and line[0] != '@': linePieces = line.split('\t') if len(linePieces) < 2: @@ -79,29 +74,32 @@ class Otu( Text ): pass return False -class Sabund( Otu ): + +class Sabund(Otu): file_ext = 'mothur.sabund' + def __init__(self, **kwd): """ - # http://www.mothur.org/wiki/Sabund_file + http://www.mothur.org/wiki/Sabund_file """ - Otu.__init__( self, **kwd ) - def init_meta( self, dataset, copy_from=None ): - Otu.init_meta( self, dataset, copy_from=copy_from ) - def sniff( self, filename ): + Otu.__init__(self, **kwd) + + def init_meta(self, dataset, copy_from=None): + Otu.init_meta(self, dataset, copy_from=copy_from) + + def sniff(self, filename): """ - Determines whether the file is a otu (operational taxonomic unit) format + Determines whether the file is otu (operational taxonomic unit) format labelcount[value(1..n)] - """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 while True: line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF if line and line[0] != '@': linePieces = line.split('\t') if len(linePieces) < 2: @@ -110,8 +108,8 @@ class Sabund( Otu ): check = int(linePieces[1]) if check + 2 != len(linePieces): return False - for i in range( 2, len(linePieces)): - ival = int(linePieces[i]) + for i in range(2, len(linePieces)): + int(linePieces[i]) except ValueError: return False count += 1 @@ -121,21 +119,22 @@ class Sabund( Otu ): pass return False -class GroupAbund( Otu ): + +class GroupAbund(Otu): file_ext = 'mothur.shared' - MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + MetadataElement(name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[]) + def __init__(self, **kwd): - Otu.__init__( self, **kwd ) - # self.column_names[0] = ['label'] - # self.column_names[1] = ['group'] - # self.column_names[2] = ['count'] + Otu.__init__(self, **kwd) + """ - def init_meta( self, dataset, copy_from=None ): - Otu.init_meta( self, dataset, copy_from=copy_from ) + def init_meta(self, dataset, copy_from=None): + Otu.init_meta(self, dataset, copy_from=copy_from) """ - def init_meta( self, dataset, copy_from=None ): - Otu.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip=1, max_data_lines = 100000, **kwd ): + def init_meta(self, dataset, copy_from=None): + Otu.init_meta(self, dataset, copy_from=copy_from) + + def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=100000, **kwd): # See if file starts with header line if dataset.has_data(): label_names = set() @@ -144,49 +143,50 @@ class GroupAbund( Otu ): comment_lines = 0 ncols = 0 try: - with open( dataset.file_name ) as fh: + with open(dataset.file_name) as fh: line = fh.readline() fields = line.strip().split('\t') - ncols = max(ncols,len(fields)) + ncols = max(ncols, len(fields)) if fields[0] == 'label' and fields[1] == 'Group': - skip=1 + skip = 1 comment_lines += 1 else: - skip=0 + skip = 0 data_lines += 1 label_names.add(fields[0]) group_names.add(fields[1]) for line in fh: data_lines += 1 fields = line.strip().split('\t') - ncols = max(ncols,len(fields)) + ncols = max(ncols, len(fields)) label_names.add(fields[0]) group_names.add(fields[1]) # Set the discovered metadata values for the dataset dataset.metadata.data_lines = data_lines dataset.metadata.columns = ncols - dataset.metadata.labels = list( label_names ) + dataset.metadata.labels = list(label_names) dataset.metadata.labels.sort() - dataset.metadata.groups = list( group_names ) + dataset.metadata.groups = list(group_names) dataset.metadata.groups.sort() dataset.metadata.skip = skip except: pass - def sniff( self, filename, vals_are_int=False): + def sniff(self, filename, vals_are_int=False): """ - Determines whether the file is a otu (operational taxonomic unit) Shared format + Determines whether the file is a otu (operational taxonomic unit) + Shared format labelgroupcount[value(1..n)] The first line is column headings as of Mothur v 1.20 """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 while True: line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF if line and line[0] != '@': linePieces = line.split('\t') if len(linePieces) < 3: @@ -196,11 +196,11 @@ class GroupAbund( Otu ): check = int(linePieces[2]) if check + 3 != len(linePieces): return False - for i in range( 3, len(linePieces)): + for i in range(3, len(linePieces)): if vals_are_int: - ival = int(linePieces[i]) + int(linePieces[i]) else: - fval = float(linePieces[i]) + float(linePieces[i]) except ValueError: return False count += 1 @@ -212,21 +212,24 @@ class GroupAbund( Otu ): pass return False + class SecondaryStructureMap(Tabular): file_ext = 'mothur.map' + def __init__(self, **kwd): """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) + Tabular.__init__(self, **kwd) self.column_names = ['Map'] - def sniff( self, filename ): + def sniff(self, filename): """ Determines whether the file is a secondary structure map format - A single column with an integer value which indicates the row that this row maps to. - check you make sure is structMap[10] = 380 then structMap[380] = 10. + A single column with an integer value which indicates the row that this + row maps to. Check to make sure if structMap[10] = 380 then + structMap[380] = 10 and vice versa. """ try: - with open( filename ) as fh: + with open(filename) as fh: line_num = 0 rowidxmap = {} while True: @@ -234,7 +237,7 @@ class SecondaryStructureMap(Tabular): line_num += 1 line = line.strip() if not line: - break #EOF + break # EOF if line: try: pointer = int(line) @@ -251,61 +254,65 @@ class SecondaryStructureMap(Tabular): return False return True -class SequenceAlignment( Fasta ): + +class SequenceAlignment(Fasta): file_ext = 'mothur.align' + def __init__(self, **kwd): - Fasta.__init__( self, **kwd ) + Fasta.__init__(self, **kwd) """Initialize AlignCheck datatype""" - def sniff( self, filename ): + def sniff(self, filename): """ Determines whether the file is in Mothur align fasta format Each sequence line must be the same length """ - try: - with open( filename ) as fh: + with open(filename) as fh: len = -1 while True: line = fh.readline() if not line: - break #EOF + break # EOF line = line.strip() - if line: #first non-empty line - if line.startswith( '>' ): - #The next line.strip() must not be '', nor startwith '>' + if line: # first non-empty line + if line.startswith('>'): + # next line.strip() must not be '', nor startwith '>' line = fh.readline().strip() - if line == '' or line.startswith( '>' ): + if line == '' or line.startswith('>'): break if len < 0: len = len(line) elif len != len(line): return False else: - break #we found a non-empty line, but its not a fasta header + # non-empty line, but its not a fasta header + break if len > 0: return True except: pass return False -class AlignCheck( Tabular ): + +class AlignCheck(Tabular): file_ext = 'mothur.align.check' + def __init__(self, **kwd): """Initialize AlignCheck datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total'] - self.column_types = ['str','int','int','int','int','int','int','int'] + Tabular.__init__(self, **kwd) + self.column_names = ['name', 'pound', 'dash', 'plus', 'equal', 'loop', 'tilde', 'total'] + self.column_types = ['str', 'int', 'int', 'int', 'int', 'int', 'int', 'int'] self.comment_lines = 1 - def set_meta( self, dataset, overwrite = True, **kwd ): - # Tabular.set_meta( self, dataset, overwrite = overwrite, first_line_is_header = True, skip = 1 ) + def set_meta(self, dataset, overwrite=True, **kwd): data_lines = 0 if dataset.has_data(): - dataset_fh = open( dataset.file_name ) + dataset_fh = open(dataset.file_name) while True: line = dataset_fh.readline() - if not line: break + if not line: + break data_lines += 1 dataset_fh.close() dataset.metadata.comment_lines = 1 @@ -313,49 +320,54 @@ class AlignCheck( Tabular ): dataset.metadata.column_names = self.column_names dataset.metadata.column_types = self.column_types + class AlignReport(Tabular): """ -QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template -AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6 + QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template + AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6 """ file_ext = 'mothur.align.report' + def __init__(self, **kwd): """Initialize AlignCheck datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['QueryName','QueryLength','TemplateName','TemplateLength','SearchMethod','SearchScore', - 'AlignmentMethod','QueryStart','QueryEnd','TemplateStart','TemplateEnd', - 'PairwiseAlignmentLength','GapsInQuery','GapsInTemplate','LongestInsert','SimBtwnQuery&Template' + Tabular.__init__(self, **kwd) + self.column_names = ['QueryName', 'QueryLength', 'TemplateName', 'TemplateLength', 'SearchMethod', 'SearchScore', + 'AlignmentMethod', 'QueryStart', 'QueryEnd', 'TemplateStart', 'TemplateEnd', + 'PairwiseAlignmentLength', 'GapsInQuery', 'GapsInTemplate', 'LongestInsert', 'SimBtwnQuery&Template' ] -class DistanceMatrix( Text ): + +class DistanceMatrix(Text): file_ext = 'mothur.dist' """Add metadata elements""" - MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?' ) + MetadataElement(name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?') - def init_meta( self, dataset, copy_from=None ): - Text.init_meta( self, dataset, copy_from=copy_from ) + def init_meta(self, dataset, copy_from=None): + Text.init_meta(self, dataset, copy_from=copy_from) - def set_meta( self, dataset, overwrite = True, skip = 0, **kwd ): - Text.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) + def set_meta(self, dataset, overwrite=True, skip=0, **kwd): + Text.set_meta(self, dataset, overwrite=overwrite, skip=skip, **kwd) try: - with open( dataset.file_name ) as fh: + with open(dataset.file_name) as fh: line = '@' while line[0] == '@': line = fh.readline().strip().strip() - dataset.metadata.sequence_count = int(line) + dataset.metadata.sequence_count = int(line) except Exception, e: log.warn("DistanceMatrix set_meta %s" % e) + class LowerTriangleDistanceMatrix(DistanceMatrix): file_ext = 'mothur.lower.dist' + def __init__(self, **kwd): """Initialize secondary structure map datatype""" - DistanceMatrix.__init__( self, **kwd ) + DistanceMatrix.__init__(self, **kwd) - def init_meta( self, dataset, copy_from=None ): - DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) + def init_meta(self, dataset, copy_from=None): + DistanceMatrix.init_meta(self, dataset, copy_from=copy_from) - def sniff( self, filename ): + def sniff(self, filename): """ Determines whether the file is a lower-triangle distance matrix (phylip) format The first line has the number of sequences in the matrix. @@ -368,7 +380,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix): U68593 0.2872 0.1690 0.3361 0.2842 """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 line = fh.readline() sequence_count = int(line.strip()) @@ -376,7 +388,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix): line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF if line: # Split into fields linePieces = line.split('\t') @@ -388,7 +400,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix): # Distances should be floats try: for linePiece in linePieces[2:]: - check = float(linePiece) + float(linePiece) except ValueError: return False # Increment line counter @@ -399,19 +411,21 @@ class LowerTriangleDistanceMatrix(DistanceMatrix): pass return False + class SquareDistanceMatrix(DistanceMatrix): file_ext = 'mothur.square.dist' def __init__(self, **kwd): - DistanceMatrix.__init__( self, **kwd ) - def init_meta( self, dataset, copy_from=None ): - DistanceMatrix.init_meta( self, dataset, copy_from=copy_from ) + DistanceMatrix.__init__(self, **kwd) - def sniff( self, filename ): + def init_meta(self, dataset, copy_from=None): + DistanceMatrix.init_meta(self, dataset, copy_from=copy_from) + + def sniff(self, filename): """ Determines whether the file is a square distance matrix (Column-formatted distance matrix) format The first line has the number of sequences in the matrix. - The following lines have the sequence name in the first column plus a column for the distance to each sequence + The following lines have the sequence name in the first column plus a column for the distance to each sequence in the row order in which they appear in the matrix. 3 U68589 0.0000 0.3371 0.3610 @@ -419,23 +433,23 @@ class SquareDistanceMatrix(DistanceMatrix): U68590 0.3371 0.0000 0.3783 """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 while True: line = fh.readline().strip() if not line: - break #EOF + break # EOF if line[0] != '@': if count == 0: seq_cnt = int(line) col_cnt = seq_cnt + 1 else: linePieces = line.split('\t') - if len(linePieces) != col_cnt : + if len(linePieces) != col_cnt: return False try: for i in range(1, col_cnt): - check = float(linePieces[i]) + float(linePieces[i]) except ValueError: return False count += 1 @@ -445,42 +459,44 @@ class SquareDistanceMatrix(DistanceMatrix): pass return False -class PairwiseDistanceMatrix(DistanceMatrix,Tabular): + +class PairwiseDistanceMatrix(DistanceMatrix, Tabular): file_ext = 'mothur.pair.dist' + def __init__(self, **kwd): """Initialize secondary structure map datatype""" - Tabular.__init__( self, **kwd ) - self.column_names = ['Sequence','Sequence','Distance'] - self.column_types = ['str','str','float'] - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): - Tabular.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd ) + Tabular.__init__(self, **kwd) + self.column_names = ['Sequence', 'Sequence', 'Distance'] + self.column_types = ['str', 'str', 'float'] - def sniff( self, filename ): + def set_meta(self, dataset, overwrite=True, skip=None, **kwd): + Tabular.set_meta(self, dataset, overwrite=overwrite, skip=skip, **kwd) + + def sniff(self, filename): """ Determines whether the file is a pairwise distance matrix (Column-formatted distance matrix) format The first and second columns have the sequence names and the third column is the distance between those sequences. """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 all_ints = True while True: line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF if line and line[0] != '@': linePieces = line.split('\t') if len(linePieces) != 3: return False try: - check = float(linePieces[2]) + float(linePieces[2]) try: # See if it's also an integer - check_int = int(linePieces[2]) + int(linePieces[2]) except ValueError: - # At least one value is not an - # integer + # At least one value is not an integer all_ints = False except ValueError: return False @@ -497,39 +513,45 @@ class PairwiseDistanceMatrix(DistanceMatrix,Tabular): class Names(Tabular): file_ext = 'mothur.names' + def __init__(self, **kwd): """ - # http://www.mothur.org/wiki/Name_file + http://www.mothur.org/wiki/Name_file Name file shows the relationship between a representative sequence(col 1) and the sequences(comma-separated) it represents(col 2) """ - Tabular.__init__( self, **kwd ) - self.column_names = ['name','representatives'] + Tabular.__init__(self, **kwd) + self.column_names = ['name', 'representatives'] self.columns = 2 + class Summary(Tabular): file_ext = 'mothur.summary' + def __init__(self, **kwd): """summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file""" - Tabular.__init__( self, **kwd ) - self.column_names = ['seqname','start','end','nbases','ambigs','polymer'] + Tabular.__init__(self, **kwd) + self.column_names = ['seqname', 'start', 'end', 'nbases', 'ambigs', 'polymer'] self.columns = 6 + class Group(Tabular): file_ext = 'mothur.groups' - MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + MetadataElement(name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[]) + def __init__(self, **kwd): """ - # http://www.mothur.org/wiki/Groups_file + http://www.mothur.org/wiki/Groups_file Group file assigns sequence (col 1) to a group (col 2) """ - Tabular.__init__( self, **kwd ) - self.column_names = ['name','group'] + Tabular.__init__(self, **kwd) + self.column_names = ['name', 'group'] self.columns = 2 - def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): + + def set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=None, **kwd): Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) - group_names = set() + group_names = set() try: - with open( dataset.file_name ) as fh: + with open(dataset.file_name) as fh: for line in fh: fields = line.strip().split('\t') try: @@ -542,37 +564,40 @@ class Group(Tabular): except: pass + class AccNos(Tabular): file_ext = 'mothur.accnos' + def __init__(self, **kwd): """A list of names""" - Tabular.__init__( self, **kwd ) + Tabular.__init__(self, **kwd) self.column_names = ['name'] self.columns = 1 -class Oligos( Text ): + +class Oligos(Text): file_ext = 'mothur.oligos' - def sniff( self, filename ): + def sniff(self, filename): """ - # http://www.mothur.org/wiki/Oligos_File + http://www.mothur.org/wiki/Oligos_File Determines whether the file is a otu (operational taxonomic unit) format """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 while True: line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF else: if line[0] != '#': linePieces = line.split('\t') - if len(linePieces) == 2 and re.match('forward|reverse',linePieces[0]): + if len(linePieces) == 2 and re.match('forward|reverse', linePieces[0]): count += 1 continue - elif len(linePieces) == 3 and re.match('barcode',linePieces[0]): + elif len(linePieces) == 3 and re.match('barcode', linePieces[0]): count += 1 continue else: @@ -585,15 +610,17 @@ class Oligos( Text ): pass return False + class Frequency(Tabular): file_ext = 'mothur.freq' + def __init__(self, **kwd): """A list of names""" - Tabular.__init__( self, **kwd ) - self.column_names = ['position','frequency'] - self.column_types = ['int','float'] + Tabular.__init__(self, **kwd) + self.column_names = ['position', 'frequency'] + self.column_types = ['int', 'float'] - def sniff( self, filename ): + def sniff(self, filename): """ Determines whether the file is a frequency tabular format for chimera analysis #1.14.0 @@ -603,13 +630,13 @@ class Frequency(Tabular): 155 0.975 """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 while True: line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF else: if count == 0 and line[0] != '#': return False @@ -618,8 +645,8 @@ class Frequency(Tabular): if len(linePieces) != 2: return False try: - i = int(linePieces[0]) - f = float(linePieces[1]) + int(linePieces[0]) + float(linePieces[1]) except: return False count += 1 @@ -629,16 +656,19 @@ class Frequency(Tabular): pass return False + class Quantile(Tabular): file_ext = 'mothur.quan' - MetadataElement( name="filtered", default=False, no_value=False, optional=True , desc="Quantiles calculated using a mask", readonly=True) - MetadataElement( name="masked", default=False, no_value=False, optional=True , desc="Quantiles calculated using a frequency filter", readonly=True) + MetadataElement(name="filtered", default=False, no_value=False, optional=True, desc="Quantiles calculated using a mask", readonly=True) + MetadataElement(name="masked", default=False, no_value=False, optional=True, desc="Quantiles calculated using a frequency filter", readonly=True) + def __init__(self, **kwd): """Quantiles for chimera analysis""" - Tabular.__init__( self, **kwd ) - self.column_names = ['num','ten','twentyfive','fifty','seventyfive','ninetyfive','ninetynine'] - self.column_types = ['int','float','float','float','float','float','float'] - def sniff( self, filename ): + Tabular.__init__(self, **kwd) + self.column_names = ['num', 'ten', 'twentyfive', 'fifty', 'seventyfive', 'ninetyfive', 'ninetynine'] + self.column_types = ['int', 'float', 'float', 'float', 'float', 'float', 'float'] + + def sniff(self, filename): """ Determines whether the file is a quantiles tabular format for chimera analysis 1 0 0 0 0 0 0 @@ -647,24 +677,24 @@ class Quantile(Tabular): ... """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 while True: line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF else: if line[0] != '#': try: linePieces = line.split('\t') - i = int(linePieces[0]) - f = float(linePieces[1]) - f = float(linePieces[2]) - f = float(linePieces[3]) - f = float(linePieces[4]) - f = float(linePieces[5]) - f = float(linePieces[6]) + int(linePieces[0]) + float(linePieces[1]) + float(linePieces[2]) + float(linePieces[3]) + float(linePieces[4]) + float(linePieces[5]) + float(linePieces[6]) count += 1 continue except: @@ -677,23 +707,24 @@ class Quantile(Tabular): pass return False + class LaneMask(Text): file_ext = 'mothur.filter' - def sniff( self, filename ): + def sniff(self, filename): """ Determines whether the file is a lane mask filter: 1 line consisting of zeros and ones. """ try: - with open( filename ) as fh: - count=0 + with open(filename) as fh: + count = 0 while True: line = fh.readline().strip() if not line: - break #EOF + break # EOF else: - count+=1 - if not re.match('^[01]+$',line): + count += 1 + if not re.match('^[01]+$', line): return False if count != 1: return False @@ -702,83 +733,87 @@ class LaneMask(Text): pass return False + class CountTable(Tabular): - MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] ) + MetadataElement(name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[]) file_ext = 'mothur.count_table' def __init__(self, **kwd): """ - # http://www.mothur.org/wiki/Count_File + http://www.mothur.org/wiki/Count_File A table with first column names and following columns integer counts # Example 1: - Representative_Sequence total + Representative_Sequence total U68630 1 U68595 1 U68600 1 # Example 2 (with group columns): - Representative_Sequence total forest pasture - U68630 1 1 0 - U68595 1 1 0 - U68600 1 1 0 - U68591 1 1 0 - U68647 1 0 1 + Representative_Sequence total forest pastur + U68630 1 1 0 + U68595 1 1 0 + U68600 1 1 0 + U68591 1 1 0 + U68647 1 0 1 """ - Tabular.__init__( self, **kwd ) - self.column_names = ['name','total'] + Tabular.__init__(self, **kwd) + self.column_names = ['name', 'total'] - def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): + def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd): try: - data_lines = 0; - with open( dataset.file_name ) as fh: + data_lines = 0 + with open(dataset.file_name) as fh: line = fh.readline() if line: line = line.strip() - colnames = line.split() + colnames = line.split() if len(colnames) > 1: - dataset.metadata.columns = len( colnames ) + dataset.metadata.columns = len(colnames) if len(colnames) > 2: dataset.metadata.groups = colnames[2:] column_types = ['str'] - for i in range(1,len(colnames)): + for i in range(1, len(colnames)): column_types.append('int') dataset.metadata.column_types = column_types dataset.metadata.comment_lines = 1 while line: line = fh.readline() - if not line: break + if not line: + break data_lines += 1 dataset.metadata.data_lines = data_lines except: pass + class RefTaxonomy(Tabular): file_ext = 'mothur.ref.taxonomy' + """ - # http://www.mothur.org/wiki/Taxonomy_outline + http://www.mothur.org/wiki/Taxonomy_outline A table with 2 or 3 columns: - SequenceName - Taxonomy (semicolon-separated taxonomy in descending order) - integer ? - Example: 2-column ( http://www.mothur.org/wiki/Taxonomy_outline ) + Example: 2-column (http://www.mothur.org/wiki/Taxonomy_outline) X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; AF052717.1 Eukaryota;Parabasalidea; - Example: 3-column ( http://vamps.mbl.edu/resources/databases.php ) + Example: 3-column (http://vamps.mbl.edu/resources/databases.php) v3_AA008 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus 5 v3_AA016 Bacteria 120 v3_AA019 Archaea;Crenarchaeota;Marine_Group_I 1 """ def __init__(self, **kwd): - Tabular.__init__( self, **kwd ) - self.column_names = ['name','taxonomy'] + Tabular.__init__(self, **kwd) + self.column_names = ['name', 'taxonomy'] - def sniff( self, filename ): + def sniff(self, filename): """ Determines whether the file is a Reference Taxonomy """ try: pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$' - with open( filename ) as fh: + with open(filename) as fh: count = 0 # VAMPS taxonomy files do not require a semicolon after the last taxonomy category # but assume assume the file will have some multi-level taxonomy assignments @@ -786,18 +821,18 @@ class RefTaxonomy(Tabular): while True: line = fh.readline() if not line: - break #EOF + break # EOF line = line.strip() if line: fields = line.split('\t') if not (2 <= len(fields) <= 3): return False - if not re.match(pat,fields[1]): + if not re.match(pat, fields[1]): return False if not found_semicolons and str(fields[1]).count(';') > 0: found_semicolons = True if len(fields) == 3: - check = int(fields[2]) + int(fields[2]) count += 1 if count > 100: break @@ -809,44 +844,50 @@ class RefTaxonomy(Tabular): pass return False + class ConsensusTaxonomy(Tabular): file_ext = 'mothur.cons.taxonomy' + def __init__(self, **kwd): """A list of names""" - Tabular.__init__( self, **kwd ) - self.column_names = ['OTU','count','taxonomy'] + Tabular.__init__(self, **kwd) + self.column_names = ['OTU', 'count', 'taxonomy'] + class TaxonomySummary(Tabular): file_ext = 'mothur.tax.summary' + def __init__(self, **kwd): """A Summary of taxon classification""" - Tabular.__init__( self, **kwd ) - self.column_names = ['taxlevel','rankID','taxon','daughterlevels','total'] + Tabular.__init__(self, **kwd) + self.column_names = ['taxlevel', 'rankID', 'taxon', 'daughterlevels', 'total'] + class Axes(Tabular): file_ext = 'mothur.axes' def __init__(self, **kwd): """Initialize axes datatype""" - Tabular.__init__( self, **kwd ) - def sniff( self, filename ): + Tabular.__init__(self, **kwd) + + def sniff(self, filename): """ Determines whether the file is an axes format The first line may have column headings. The following lines have the name in the first column plus float columns for each axis. - ==> 98_sq_phylip_amazon.fn.unique.pca.axes <== - group axis1 axis2 - forest 0.000000 0.145743 - pasture 0.145743 0.000000 - - ==> 98_sq_phylip_amazon.nmds.axes <== - axis1 axis2 - U68589 0.262608 -0.077498 - U68590 0.027118 0.195197 - U68591 0.329854 0.014395 + ==> 98_sq_phylip_amazon.fn.unique.pca.axes <== + group axis1 axis2 + forest 0.000000 0.145743 + pasture 0.145743 0.000000 + + ==> 98_sq_phylip_amazon.nmds.axes <== + axis1 axis2 + U68589 0.262608 -0.077498 + U68590 0.027118 0.195197 + U68591 0.329854 0.014395 """ try: - with open( filename ) as fh: + with open(filename) as fh: count = 0 line = fh.readline() line = line.strip() @@ -856,16 +897,16 @@ class Axes(Tabular): line = fh.readline() line = line.strip() if not line: - break #EOF + break # EOF if line: fields = line.split('\t') - if col_cnt == None: # ignore values in first line as they may be column headings + if col_cnt is None: # ignore values in first line as they may be column headings col_cnt = len(fields) # There should be at least 2 columns if col_cnt < 2: return False - else: - if len(fields) != col_cnt : + else: + if len(fields) != col_cnt: return False try: for i in range(1, col_cnt): @@ -893,13 +934,14 @@ class Axes(Tabular): pass return False + class SffFlow(Tabular): - MetadataElement( name="flow_values", default="", no_value="", optional=True , desc="Total number of flow values", readonly=True) - MetadataElement( name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False) + MetadataElement(name="flow_values", default="", no_value="", optional=True, desc="Total number of flow values", readonly=True) + MetadataElement(name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False) file_ext = 'mothur.sff.flow' """ - # http://www.mothur.org/wiki/Flow_file - The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400. + http://www.mothur.org/wiki/Flow_file + The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400. Following lines contain: - SequenceName - the number of useable flows as defined by 454's software @@ -907,16 +949,16 @@ class SffFlow(Tabular): Example: 800 GQY1XT001CQL4K 85 1.04 0.00 1.00 0.02 0.03 1.02 0.05 ... - GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 ... + GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 ... GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ... """ def __init__(self, **kwd): - Tabular.__init__( self, **kwd ) + Tabular.__init__(self, **kwd) - def set_meta( self, dataset, overwrite = True, skip = 1, max_data_lines = None, **kwd ): + def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd): Tabular.set_meta(self, dataset, overwrite, 1, max_data_lines) try: - with open( dataset.file_name ) as fh: + with open(dataset.file_name) as fh: line = fh.readline() line = line.strip() flow_values = int(line) @@ -924,26 +966,21 @@ class SffFlow(Tabular): except: pass - def make_html_table( self, dataset, skipchars=[] ): + def make_html_table(self, dataset, skipchars=[]): """Create HTML table, used for displaying peek""" out = [''] - comments = [] try: # Generate column header out.append('') - out.append( '' % 1 ) - out.append( '' % 2 ) - for i in range( 3, dataset.metadata.columns+1 ): - base = dataset.metadata.flow_order[(i+1)%4] - out.append( '' % (i-2,base) ) + out.append('' % 1) + out.append('' % 2) + for i in range(3, dataset.metadata.columns+1): + base = dataset.metadata.flow_order[(i+1) % 4] + out.append('' % (i-2, base)) out.append('') - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '
%d. Name%d. Flows%d. %d %s%d. Name%d. Flows%d. %d %s
' ) - out = "".join( out ) + out.append(self.make_html_peek_rows(dataset, skipchars=skipchars)) + out.append('') + out = "".join(out) except Exception, exc: - out = "Can't create peek %s" % str( exc ) + out = "Can't create peek %s" % str(exc) return out - -if __name__ == '__main__': - import doctest, sys - doctest.testmod(sys.modules[__name__]) From 31129e9d18b52eb9842a0ebbfe1eabbaedc73334 Mon Sep 17 00:00:00 2001 From: shiltemann Date: Thu, 31 Mar 2016 14:42:55 +0200 Subject: [PATCH 12/18] subclass mothur.align --- config/datatypes_conf.xml.sample | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index 1b487f4a984..a2216a69f35 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -502,7 +502,7 @@ - + From 43f7564365ac101bfd43c55b741b1543eed6457d Mon Sep 17 00:00:00 2001 From: shiltemann Date: Thu, 31 Mar 2016 14:47:21 +0200 Subject: [PATCH 13/18] update sniffers and add doctests --- lib/galaxy/datatypes/mothur.py | 792 +++++++++--------- .../mothur_datatypetest_false.mothur.axes | 42 + .../mothur_datatypetest_false.mothur.filter | 1 + .../mothur_datatypetest_false.mothur.freq | 42 + ...othur_datatypetest_false.mothur.lower.dist | 84 ++ .../test/mothur_datatypetest_false.mothur.map | 18 + .../mothur_datatypetest_false.mothur.oligos | 12 + .../test/mothur_datatypetest_false.mothur.otu | 37 + ...mothur_datatypetest_false.mothur.pair.dist | 42 + .../mothur_datatypetest_false.mothur.quan | 42 + ...hur_datatypetest_false.mothur.ref.taxonomy | 42 + .../mothur_datatypetest_false.mothur.sabund | 5 + .../mothur_datatypetest_false.mothur.shared | 3 + ...thur_datatypetest_false.mothur.square.dist | 42 + .../test/mothur_datatypetest_true.mothur.axes | 42 + .../mothur_datatypetest_true.mothur.filter | 1 + .../test/mothur_datatypetest_true.mothur.freq | 42 + ...mothur_datatypetest_true.mothur.lower.dist | 99 +++ .../test/mothur_datatypetest_true.mothur.map | 18 + .../mothur_datatypetest_true.mothur.oligos | 12 + .../test/mothur_datatypetest_true.mothur.otu | 37 + .../mothur_datatypetest_true.mothur.pair.dist | 42 + .../test/mothur_datatypetest_true.mothur.quan | 42 + ...thur_datatypetest_true.mothur.ref.taxonomy | 42 + .../mothur_datatypetest_true.mothur.sabund | 5 + .../mothur_datatypetest_true.mothur.shared | 3 + ...othur_datatypetest_true.mothur.square.dist | 99 +++ 27 files changed, 1281 insertions(+), 407 deletions(-) create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared create mode 100644 lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index 8b6cca7e244..a1deb110ff4 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -4,10 +4,10 @@ Mothur Metagenomics Datatypes import logging import sys import re +from galaxy.datatypes.sniff import get_headers from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.data import Text from galaxy.datatypes.tabular import Tabular -from galaxy.datatypes.sequence import Fasta log = logging.getLogger(__name__) @@ -47,31 +47,32 @@ class Otu(Text): def sniff(self, filename): """ Determines whether the file is otu (operational taxonomic unit) format + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.otu' ) + >>> Otu().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.otu' ) + >>> Otu().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - if line and line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 2: + headers = get_headers(filename, sep='\t') + count = 0 + for line in headers: + if not line[0].startswith('@'): + if len(line) < 2: + return False + if count >= 1: + try: + check = int(line[1]) + if check + 2 != len(line): return False - if count >= 1: - try: - check = int(linePieces[1]) - if check + 2 != len(linePieces): - return False - except ValueError: - return False - count += 1 - if count > 2: - return True - except: - pass + except ValueError: + return False + count += 1 + if count > 2: + return True + return False @@ -91,32 +92,33 @@ class Sabund(Otu): """ Determines whether the file is otu (operational taxonomic unit) format labelcount[value(1..n)] + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.sabund' ) + >>> Sabund().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.sabund' ) + >>> Sabund().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - if line and line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 2: - return False - try: - check = int(linePieces[1]) - if check + 2 != len(linePieces): - return False - for i in range(2, len(linePieces)): - int(linePieces[i]) - except ValueError: - return False - count += 1 - if count > 0: - return True - except: - pass + headers = get_headers(filename, sep='\t') + count = 0 + for line in headers: + if not line[0].startswith('@'): + if len(line) < 2: + return False + try: + check = int(line[1]) + if check + 2 != len(line): + return False + for i in range(2, len(line)): + int(line[i]) + except ValueError: + return False + count += 1 + if count > 0: + return True + return False @@ -177,39 +179,37 @@ class GroupAbund(Otu): Determines whether the file is a otu (operational taxonomic unit) Shared format labelgroupcount[value(1..n)] - The first line is column headings as of Mothur v 1.20 + The first line is column headings as of Mothur v 1.2 + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.shared' ) + >>> GroupAbund().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.shared' ) + >>> GroupAbund().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - if line and line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) < 3: + headers = get_headers(filename, sep='\t') + count = 0 + for line in headers: + if not line[0].startswith('@'): + if len(line) < 3: + return False + if count > 0 or line[0] != 'label': + try: + check = int(line[2]) + if check + 3 != len(line): return False - if count > 0 or linePieces[0] != 'label': - try: - check = int(linePieces[2]) - if check + 3 != len(linePieces): - return False - for i in range(3, len(linePieces)): - if vals_are_int: - int(linePieces[i]) - else: - float(linePieces[i]) - except ValueError: - return False - count += 1 - if count >= 5: - return True - if count < 5 and count > 0: - return True - except: - pass + for i in range(3, len(line)): + if vals_are_int: + int(line[i]) + else: + float(line[i]) + except ValueError: + return False + count += 1 + if count > 1: + return True return False @@ -227,74 +227,36 @@ class SecondaryStructureMap(Tabular): A single column with an integer value which indicates the row that this row maps to. Check to make sure if structMap[10] = 380 then structMap[380] = 10 and vice versa. + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.map' ) + >>> SecondaryStructureMap().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.map' ) + >>> SecondaryStructureMap().sniff( fname ) + False """ - try: - with open(filename) as fh: - line_num = 0 - rowidxmap = {} - while True: - line = fh.readline() - line_num += 1 - line = line.strip() - if not line: - break # EOF - if line: - try: - pointer = int(line) - if pointer > line_num: - rowidxmap[pointer] = line_num - elif pointer > 0 or line_num in rowidxmap: - if rowidxmap[line_num] != pointer: - return False - except ValueError: - return False - except: - return False + headers = get_headers(filename, sep='\t') + line_num = 0 + rowidxmap = {} + for line in headers: + line_num += 1 + if len(line) > 1: + return False + try: + pointer = int(line[0]) + if pointer > line_num: + rowidxmap[pointer] = line_num + elif pointer > 0 or line_num in rowidxmap: + if rowidxmap[line_num] != pointer: + return False + except (ValueError, KeyError): + return False if line_num < 3: return False return True -class SequenceAlignment(Fasta): - file_ext = 'mothur.align' - - def __init__(self, **kwd): - Fasta.__init__(self, **kwd) - """Initialize AlignCheck datatype""" - - def sniff(self, filename): - """ - Determines whether the file is in Mothur align fasta format - Each sequence line must be the same length - """ - try: - with open(filename) as fh: - len = -1 - while True: - line = fh.readline() - if not line: - break # EOF - line = line.strip() - if line: # first non-empty line - if line.startswith('>'): - # next line.strip() must not be '', nor startwith '>' - line = fh.readline().strip() - if line == '' or line.startswith('>'): - break - if len < 0: - len = len(line) - elif len != len(line): - return False - else: - # non-empty line, but its not a fasta header - break - if len > 0: - return True - except: - pass - return False - - class AlignCheck(Tabular): file_ext = 'mothur.align.check' @@ -372,43 +334,51 @@ class LowerTriangleDistanceMatrix(DistanceMatrix): Determines whether the file is a lower-triangle distance matrix (phylip) format The first line has the number of sequences in the matrix. The remaining lines have the sequence name followed by a list of distances from all preceeding sequences - 5 + 5 # possibly but not always preceded by a tab :/ U68589 U68590 0.3371 U68591 0.3609 0.3782 U68592 0.4155 0.3197 0.4148 U68593 0.2872 0.1690 0.3361 0.2842 + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.lower.dist' ) + >>> LowerTriangleDistanceMatrix().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.lower.dist' ) + >>> LowerTriangleDistanceMatrix().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - line = fh.readline() - sequence_count = int(line.strip()) - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - if line: - # Split into fields - linePieces = line.split('\t') - # Each line should have the same number of - # fields as the Python line index - linePieces = line.split('\t') - if len(linePieces) != (count + 1): - return False - # Distances should be floats + numlines = 300 + headers = get_headers(filename, sep='\t', count=numlines) + line_num = 0 + for line in headers: + if not line[0].startswith('@'): + # first line should contain the number of sequences in the file + if line_num == 0: + if len(line) > 2: + return False + else: try: - for linePiece in linePieces[2:]: - float(linePiece) + sequence_count = int(''.join(line)) except ValueError: return False - # Increment line counter - count += 1 - if count > 2: - return True - except: - pass + else: + # number of fields should equal the line number + if len(line) != (line_num): + return False + try: + # Distances should be floats + for column in line[2:]: + float(column) + except ValueError: + return False + line_num += 1 + + # check if the number of lines in the file was as expected + if line_num == sequence_count + 1 or line_num == numlines + 1: + return True + return False @@ -431,32 +401,44 @@ class SquareDistanceMatrix(DistanceMatrix): U68589 0.0000 0.3371 0.3610 U68590 0.3371 0.0000 0.3783 U68590 0.3371 0.0000 0.3783 + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.square.dist' ) + >>> SquareDistanceMatrix().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.square.dist' ) + >>> SquareDistanceMatrix().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline().strip() - if not line: - break # EOF - if line[0] != '@': - if count == 0: - seq_cnt = int(line) - col_cnt = seq_cnt + 1 - else: - linePieces = line.split('\t') - if len(linePieces) != col_cnt: - return False - try: - for i in range(1, col_cnt): - float(linePieces[i]) - except ValueError: - return False - count += 1 - if count > 2: - return True - except: - pass + numlines = 300 + headers = get_headers(filename, sep='\t', count=numlines) + line_num = 0 + for line in headers: + if not line[0].startswith('@'): + if line_num == 0: + if len(line) > 2: + return False + else: + try: + sequence_count = int(''.join(line)) + except ValueError: + return False + else: + # number of fields should equal the number of sequences + if len(line) != sequence_count + 1: + return False + try: + # Distances should be floats + for column in line[2:]: + float(column) + except ValueError: + return False + line_num += 1 + + # check if the number of lines in the file was as expected + if line_num == sequence_count + 1 or line_num == numlines + 1: + return True + return False @@ -476,38 +458,36 @@ class PairwiseDistanceMatrix(DistanceMatrix, Tabular): """ Determines whether the file is a pairwise distance matrix (Column-formatted distance matrix) format The first and second columns have the sequence names and the third column is the distance between those sequences. + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.pair.dist' ) + >>> PairwiseDistanceMatrix().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.pair.dist' ) + >>> PairwiseDistanceMatrix().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - all_ints = True - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - if line and line[0] != '@': - linePieces = line.split('\t') - if len(linePieces) != 3: - return False - try: - float(linePieces[2]) - try: - # See if it's also an integer - int(linePieces[2]) - except ValueError: - # At least one value is not an integer - all_ints = False - except ValueError: - return False - count += 1 - if count > 2: - if not all_ints: - return True - else: + headers = get_headers(filename, sep='\t') + count = 0 + for line in headers: + if not line[0].startswith('@'): + if len(line) != 3: return False - except: - pass + try: + float(line[2]) + try: + # See if it's also an integer + int(line[2]) + except ValueError: + # At least one value is not an integer + all_ints = False + except ValueError: + return False + count += 1 + + if count > 2: + return not all_ints + return False @@ -582,32 +562,30 @@ class Oligos(Text): """ http://www.mothur.org/wiki/Oligos_File Determines whether the file is a otu (operational taxonomic unit) format + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.oligos' ) + >>> Oligos().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.oligos' ) + >>> Oligos().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - else: - if line[0] != '#': - linePieces = line.split('\t') - if len(linePieces) == 2 and re.match('forward|reverse', linePieces[0]): - count += 1 - continue - elif len(linePieces) == 3 and re.match('barcode', linePieces[0]): - count += 1 - continue - else: - return False - if count > 20: - return True - if count > 0: - return True - except: - pass + headers = get_headers(filename, sep='\t') + count = 0 + for line in headers: + if not line[0].startswith('@') and not line[0].startswith('#'): + if len(line) == 2 and re.match('forward|reverse', line[0]): + count += 1 + continue + elif len(line) == 3 and re.match('barcode', line[0]): + count += 1 + continue + else: + return False + if count > 0: + return True + return False @@ -628,32 +606,36 @@ class Frequency(Tabular): 1 0.000 ... 155 0.975 + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.freq' ) + >>> Frequency().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.freq' ) + >>> Frequency().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - else: - if count == 0 and line[0] != '#': - return False - if line[0] != '#': - linePieces = line.split('\t') - if len(linePieces) != 2: - return False - try: - int(linePieces[0]) - float(linePieces[1]) - except: - return False - count += 1 - if count > 0: - return True - except: - pass + headers = get_headers(filename, sep='\t') + count = 0 + for line in headers: + if not line[0].startswith('@'): + if count == 0: + # first line should be # + if not line[0].startswith('#') and len(line) == 1: + return False + else: + # all other lines should be + if len(line) != 2: + return False + try: + int(line[0]) + float(line[1]) + except: + return False + count += 1 + if count > 1: + return True + return False @@ -675,36 +657,35 @@ class Quantile(Tabular): 2 0.309198 0.309198 0.37161 0.37161 0.37161 0.37161 3 0.510982 0.563213 0.693529 0.858939 1.07442 1.20608 ... + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.quan' ) + >>> Quantile().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.quan' ) + >>> Quantile().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - else: - if line[0] != '#': - try: - linePieces = line.split('\t') - int(linePieces[0]) - float(linePieces[1]) - float(linePieces[2]) - float(linePieces[3]) - float(linePieces[4]) - float(linePieces[5]) - float(linePieces[6]) - count += 1 - continue - except: - return False - if count > 10: - return True - if count > 0: - return True - except: - pass + headers = get_headers(filename, sep='\t') + count = 0 + for line in headers: + if not line[0].startswith('@') and not line[0].startswith('#'): + if len(line) != 7: + return False + try: + int(line[0]) + float(line[1]) + float(line[2]) + float(line[3]) + float(line[4]) + float(line[5]) + float(line[6]) + except: + return False + count += 1 + if count > 0: + return True + return False @@ -714,24 +695,23 @@ class LaneMask(Text): def sniff(self, filename): """ Determines whether the file is a lane mask filter: 1 line consisting of zeros and ones. + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.filter' ) + >>> LaneMask().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.filter' ) + >>> LaneMask().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - while True: - line = fh.readline().strip() - if not line: - break # EOF - else: - count += 1 - if not re.match('^[01]+$', line): - return False - if count != 1: - return False - return True - except: - pass - return False + headers = get_headers(filename, sep='\t') + if len(headers) != 1 or len(headers[0]) != 1: + return False + + if not re.match('^[01]+$', headers[0][0]): + return False + + return True class CountTable(Tabular): @@ -788,7 +768,14 @@ class CountTable(Tabular): class RefTaxonomy(Tabular): file_ext = 'mothur.ref.taxonomy' - """ + def __init__(self, **kwd): + Tabular.__init__(self, **kwd) + self.column_names = ['name', 'taxonomy'] + + def sniff(self, filename): + """ + Determines whether the file is a Reference Taxonomy + http://www.mothur.org/wiki/Taxonomy_outline A table with 2 or 3 columns: - SequenceName @@ -802,46 +789,38 @@ class RefTaxonomy(Tabular): v3_AA008 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus 5 v3_AA016 Bacteria 120 v3_AA019 Archaea;Crenarchaeota;Marine_Group_I 1 - """ - def __init__(self, **kwd): - Tabular.__init__(self, **kwd) - self.column_names = ['name', 'taxonomy'] - def sniff(self, filename): + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.ref.taxonomy' ) + >>> RefTaxonomy().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.ref.taxonomy' ) + >>> RefTaxonomy().sniff( fname ) + False """ - Determines whether the file is a Reference Taxonomy - """ - try: - pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$' - with open(filename) as fh: - count = 0 - # VAMPS taxonomy files do not require a semicolon after the last taxonomy category - # but assume assume the file will have some multi-level taxonomy assignments - found_semicolons = False - while True: - line = fh.readline() - if not line: - break # EOF - line = line.strip() - if line: - fields = line.split('\t') - if not (2 <= len(fields) <= 3): - return False - if not re.match(pat, fields[1]): - return False - if not found_semicolons and str(fields[1]).count(';') > 0: - found_semicolons = True - if len(fields) == 3: - int(fields[2]) - count += 1 - if count > 100: - break - if count > 0: - # This will be true if at least one entry - # has semicolons in the 2nd column - return found_semicolons - except: - pass + headers = get_headers(filename, sep='\t', count=300) + count = 0 + pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$' + found_semicolons = False + for line in headers: + if not line[0].startswith('@') and not line[0].startswith('#'): + if not (2 <= len(line) <= 3): + return False + if not re.match(pat, line[1]): + return False + if not found_semicolons and str(line[1]).count(';') > 0: + found_semicolons = True + if len(line) == 3: + try: + int(line[2]) + except: + return False + count += 1 + + if count > 0: + # Require that at least one entry has semicolons in the 2nd column + return found_semicolons + return False @@ -880,58 +859,52 @@ class Axes(Tabular): forest 0.000000 0.145743 pasture 0.145743 0.000000 - ==> 98_sq_phylip_amazon.nmds.axes <== + ==> 98_sq_phylip_amazon.nmds.axes <== axis1 axis2 U68589 0.262608 -0.077498 U68590 0.027118 0.195197 U68591 0.329854 0.014395 + + >>> from galaxy.datatypes.sniff import get_test_fname + >>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.axes' ) + >>> Axes().sniff( fname ) + True + >>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.axes' ) + >>> Axes().sniff( fname ) + False """ - try: - with open(filename) as fh: - count = 0 - line = fh.readline() - line = line.strip() - col_cnt = None - all_integers = True - while True: - line = fh.readline() - line = line.strip() - if not line: - break # EOF - if line: - fields = line.split('\t') - if col_cnt is None: # ignore values in first line as they may be column headings - col_cnt = len(fields) - # There should be at least 2 columns - if col_cnt < 2: - return False - else: - if len(fields) != col_cnt: - return False - try: - for i in range(1, col_cnt): - check = float(fields[i]) - # Check abs value is <= 1.0 - if abs(check) > 1.0: - return False - # Also test for whether value is an integer - try: - check = int(fields[i]) - except ValueError: - all_integers = False - except ValueError: - return False - count += 1 - if count > 10: - break - if count > 0: - if not all_integers: - # At least one value was a float - return True - else: - return False - except: - pass + headers = get_headers(filename, sep='\t') + count = 0 + col_cnt = None + all_integers = True + for line in headers: + if count == 0: + pass + elif col_cnt is None: + col_cnt = len(line) + if col_cnt < 2: + return False + else: + if len(line) != col_cnt: + return False + try: + for i in range(1, col_cnt): + check = float(line[i]) + # Check abs value is <= 1.0 + if abs(check) > 1.0: + return False + # Also test for whether value is an integer + try: + check = int(line[i]) + except ValueError: + all_integers = False + except ValueError: + return False + count += 1 + + if count > 0: + return not all_integers + return False @@ -984,3 +957,8 @@ class SffFlow(Tabular): except Exception, exc: out = "Can't create peek %s" % str(exc) return out + + +if __name__ == '__main__': + import doctest + doctest.testmod(sys.modules[__name__]) diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes new file mode 100644 index 00000000000..1e544a338d0 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes @@ -0,0 +1,42 @@ +group axis1 axis2 axis3 axis4 axis5 axis6 axis7 axis8 axis9 axis10 axis11 axis12 axis13 axis14 axis15 axis16 axis17 axis18 axis19 axis20 axis21 axis22 axis23 axis24 axis25 axis26 axis27 axis28 axis29 axis30 axis31 axis32 axis33 axis34 axis35 axis36 axis37 axis38 axis39 axis40 axis41 axis42 axis43 axis44 axis45 axis46 axis47 axis48 axis49 axis50 axis51 axis52 axis53 axis54 axis55 axis56 axis57 axis58 axis59 axis60 axis61 axis62 axis63 axis64 axis65 axis66 axis67 axis68 axis69 axis70 axis71 axis72 axis73 axis74 axis75 axis76 axis77 axis78 axis79 axis80 axis81 axis82 axis83 axis84 axis85 axis86 axis87 axis88 axis89 axis90 axis91 axis92 axis93 axis94 axis95 axis96 axis97 axis98 +U68589 0.064970 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+forward CCGTCAATTCMTTTRAGT +barcode AATGGTAC F003D000 +barcode AACCTGGC F003D002 +barcode TTCGTGGC F003D004 +barcode TTCTTGAC F003D006 +barcode TTCGCGAC F003D008 +barcode TCCAGAAC F003D142 +barcode AAGGCCTC F003D144 +tardis TGACCGTC F003D146 +barcode AGGTTGTC F003D148 +barcode TGGTGAAC F003D150 +barcode AACCGTGTC MOCK.GQY1XT001 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu new file mode 100644 index 00000000000..4c0ab12054f --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu @@ -0,0 +1,37 @@ +label numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 Otu11 Otu12 Otu13 Otu14 Otu15 Otu16 Otu17 Otu18 Otu19 Otu20 Otu21 Otu22 Otu23 Otu24 Otu25 Otu26 Otu27 Otu28 Otu29 Otu30 Otu31 Otu32 Otu33 Otu34 Otu35 Otu36 Otu37 Otu38 Otu39 Otu40 Otu41 Otu42 Otu43 Otu44 Otu45 Otu46 Otu47 Otu48 Otu49 Otu50 Otu51 Otu52 Otu53 Otu54 Otu55 Otu56 Otu57 Otu58 Otu59 Otu60 Otu61 Otu62 Otu63 Otu64 Otu65 Otu66 Otu67 Otu68 Otu69 Otu70 Otu71 Otu72 Otu73 Otu74 Otu75 Otu76 Otu77 Otu78 Otu79 Otu80 Otu81 Otu82 Otu83 Otu84 Otu85 Otu86 Otu87 Otu88 Otu89 Otu90 Otu91 Otu92 Otu93 Otu94 Otu95 Otu96 Otu97 Otu98 +unique 96 U68667,U68641 U68620,U68618 U68663 U68662 U68661 U68660 U68659 U68658 U68657 U68656 U68655 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68688 U68687 U68686 U68685 U68684 U68683 U68682 U68681 U68680 U68679 U68678 U68677 U68676 U68675 U68674 U68673 U68672 U68671 U68670 U68669 U68668 U68666 U68665 U68664 U68613 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68638 U68637 U68636 U68635 U68634 U68633 U68632 U68631 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68615 U68614 +0.01 93 U68688,U68665 U68636,U68631 U68667,U68641 U68620,U68618 U68680,U68615 U68661 U68660 U68659 U68658 U68657 U68656 U68655 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68687 U68686 U68685 U68684 U68683 U68682 U68681 U68679 U68678 U68677 U68676 U68675 U68674 U68673 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68663 U68662 U68613 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68638 U68637 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68614 +0.02 90 U68688,U68665,U68679,U68663 U68673,U68667,U68641 U68636,U68631 U68620,U68618 U68680,U68615 U68658 U68657 U68656 U68655 U68686 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68638 U68687 U68683 U68682 U68681 U68684 U68678 U68677 U68676 U68675 U68674 U68685 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68662 U68661 U68660 U68659 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68637 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68614 U68613 +0.03 88 U68688,U68665,U68679,U68663 U68658,U68638,U68620,U68618 U68673,U68667,U68641 U68636,U68631 U68680,U68615 U68686 U68657 U68656 U68655 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68637 U68687 U68683 U68682 U68681 U68684 U68678 U68677 U68676 U68675 U68674 U68685 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68662 U68661 U68660 U68659 U68613 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68614 +0.04 83 U68688,U68665,U68679,U68663 U68658,U68638,U68620,U68618 U68673,U68667,U68641 U68636,U68631 U68637,U68602 U68652,U68610 U68614,U68596 U68678,U68619 U68680,U68615 U68681,U68677 U68656 U68655 U68654 U68653 U68685 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68686 U68687 U68676 U68675 U68674 U68682 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68662 U68661 U68660 U68683 U68659 U68684 U68657 U68613 U68612 U68611 U68609 U68608 U68607 U68606 U68605 U68603 U68601 U68600 U68599 U68598 U68597 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68616 U68617 U68622 U68621 +0.05 78 U68688,U68665,U68679,U68663 U68658,U68638,U68620,U68618 U68683,U68652,U68610 U68673,U68667,U68641 U68636,U68631 U68637,U68602 U68628,U68601 U68614,U68596 U68666,U68595 U68672,U68621 U68686,U68635 U68678,U68619 U68680,U68615 U68681,U68677 U68654 U68653 U68651 U68649 U68648 U68647 U68646 U68645 U68685 U68644 U68643 U68642 U68640 U68639 U68687 U68676 U68675 U68674 U68671 U68670 U68669 U68668 U68664 U68662 U68661 U68660 U68682 U68659 U68684 U68657 U68656 U68655 U68607 U68608 U68600 U68609 U68599 U68606 U68598 U68611 U68612 U68613 U68605 U68616 U68617 U68597 U68603 U68594 U68589 U68634 U68590 U68633 U68632 U68591 U68592 U68630 U68629 U68627 U68626 U68625 U68624 U68623 U68622 U68593 +0.06 69 U68688,U68665,U68679,U68663 U68683,U68652,U68610,U68671 U68658,U68638,U68620,U68618 U68673,U68667,U68641,U68598 U68634,U68628,U68601 U68678,U68619,U68645 U68636,U68631 U68633,U68612 U68637,U68602 U68627,U68609 U68648,U68632 U68614,U68596 U68666,U68595 U68605,U68597 U68672,U68621 U68686,U68635 U68681,U68677 U68680,U68615 U68676,U68660 U68649 U68647 U68646 U68644 U68682 U68643 U68642 U68640 U68639 U68684 U68685 U68687 U68651 U68653 U68654 U68655 U68656 U68657 U68659 U68661 U68662 U68664 U68675 U68668 U68669 U68670 U68674 U68608 U68607 U68606 U68603 U68611 U68600 U68613 U68599 U68616 U68617 U68622 U68623 U68589 U68590 U68591 U68592 U68630 U68593 U68629 U68594 U68626 U68625 U68624 +0.07 65 U68678,U68619,U68645,U68673,U68667,U68641,U68598 U68688,U68665,U68679,U68663 U68683,U68652,U68610,U68671 U68658,U68638,U68620,U68618 U68634,U68628,U68601 U68617,U68614,U68596 U68633,U68612 U68636,U68631 U68637,U68602 U68627,U68609 U68648,U68632 U68666,U68595 U68605,U68597 U68687,U68592 U68686,U68635 U68682,U68657 U68681,U68677 U68680,U68615 U68676,U68660 U68672,U68621 U68670 U68685 U68684 U68639 U68640 U68674 U68642 U68643 U68644 U68646 U68647 U68669 U68649 U68651 U68653 U68668 U68654 U68655 U68656 U68675 U68659 U68661 U68662 U68664 U68608 U68607 U68606 U68603 U68611 U68613 U68600 U68599 U68616 U68622 U68623 U68589 U68590 U68591 U68630 U68629 U68593 U68594 U68626 U68625 U68624 +0.08 56 U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618 U68688,U68665,U68679,U68663,U68653,U68676,U68660 U68666,U68595,U68636,U68631 U68683,U68652,U68610,U68671 U68617,U68614,U68596 U68634,U68628,U68601 U68686,U68635,U68613 U68649,U68639 U68651,U68640 U68654,U68593 U68687,U68592 U68648,U68632 U68605,U68597 U68637,U68602 U68672,U68621 U68626,U68623 U68627,U68609 U68633,U68612 U68680,U68615 U68681,U68677 U68682,U68657 U68630 U68642 U68643 U68644 U68646 U68647 U68655 U68656 U68659 U68661 U68662 U68664 U68668 U68669 U68670 U68674 U68675 U68684 U68685 U68589 U68590 U68591 U68594 U68599 U68600 U68603 U68606 U68607 U68608 U68611 U68616 U68622 U68629 U68624 U68625 +0.09 55 U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618 U68688,U68665,U68679,U68663,U68653,U68676,U68660 U68686,U68635,U68613,U68637,U68602 U68666,U68595,U68636,U68631 U68683,U68652,U68610,U68671 U68617,U68614,U68596 U68634,U68628,U68601 U68651,U68640 U68654,U68593 U68649,U68639 U68687,U68592 U68648,U68632 U68605,U68597 U68627,U68609 U68672,U68621 U68633,U68612 U68626,U68623 U68682,U68657 U68680,U68615 U68681,U68677 U68642 U68643 U68630 U68644 U68646 U68647 U68655 U68656 U68659 U68661 U68662 U68664 U68668 U68669 U68670 U68674 U68675 U68684 U68685 U68589 U68590 U68591 U68594 U68599 U68600 U68603 U68606 U68607 U68608 U68611 U68616 U68622 U68629 U68624 U68625 +0.10 49 U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618 U68688,U68665,U68679,U68663,U68653,U68676,U68660 U68654,U68593,U68649,U68639,U68606 U68629,U68617,U68614,U68596 U68683,U68652,U68610,U68671 U68634,U68628,U68601,U68607 U68648,U68632,U68605,U68597 U68666,U68595,U68636,U68631 U68626,U68623 U68627,U68609 U68633,U68612 U68651,U68640 U68687,U68592 U68682,U68657 U68681,U68677 U68680,U68615 U68672,U68621 U68670 U68685 U68684 U68630 U68669 U68668 U68642 U68643 U68644 U68646 U68647 U68675 U68674 U68655 U68656 U68659 U68661 U68662 U68664 U68589 U68590 U68591 U68594 U68599 U68600 U68603 U68608 U68611 U68616 U68625 U68624 U68622 +0.11 45 U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618 U68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647 U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596 U68654,U68593,U68649,U68639,U68606 U68648,U68632,U68605,U68597 U68666,U68595,U68636,U68631 U68683,U68652,U68610,U68671 U68682,U68657,U68675 U68680,U68615,U68670 U68687,U68592 U68651,U68640 U68633,U68612 U68627,U68609 U68672,U68621 U68626,U68623 U68681,U68677 U68630 U68625 U68642 U68643 U68644 U68646 U68624 U68655 U68656 U68659 U68661 U68662 U68664 U68668 U68669 U68674 U68684 U68685 U68608 U68603 U68611 U68600 U68616 U68599 U68594 U68589 U68622 U68590 U68591 +0.12 43 U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659 U68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647 U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596 U68654,U68593,U68649,U68639,U68606 U68648,U68632,U68605,U68597 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U68664 U68668 U68669 U68674 U68684 U68589 U68590 U68599 U68608 U68594 U68603 U68611 U68616 +0.14 36 U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655 U68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647 U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631 U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596 U68684,U68654,U68593,U68649,U68639,U68606 U68682,U68657,U68675,U68627,U68609 U68648,U68632,U68605,U68597 U68687,U68592,U68685 U68680,U68615,U68670 U68651,U68640 U68633,U68612 U68626,U68623 U68600,U68591 U68646,U68590 U68672,U68621 U68681,U68677 U68643 U68642 U68630 U68625 U68622 U68644 U68656 U68661 U68662 U68664 U68668 U68669 U68674 U68599 U68611 U68603 U68608 U68616 U68594 U68589 +0.15 35 U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640 U68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647 U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631 U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596 U68684,U68654,U68593,U68649,U68639,U68606 U68682,U68657,U68675,U68627,U68609 U68648,U68632,U68605,U68597 U68687,U68592,U68685 U68680,U68615,U68670 U68681,U68677 U68672,U68621 U68646,U68590 U68600,U68591 U68626,U68623 U68633,U68612 U68643 U68642 U68630 U68625 U68622 U68644 U68656 U68661 U68662 U68664 U68668 U68669 U68674 U68599 U68611 U68608 U68603 U68616 U68594 U68589 +0.16 34 U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640 U68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647 U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631 U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596 U68684,U68654,U68593,U68649,U68639,U68606 U68682,U68657,U68675,U68627,U68609 U68648,U68632,U68605,U68597 U68687,U68592,U68685 U68681,U68677,U68669 U68680,U68615,U68670 U68646,U68590 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blub diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan new file mode 100644 index 00000000000..b189c71ab7e --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan @@ -0,0 +1,42 @@ +#1.36.1 +1 0 0 0 0 0 0 +2 0.049144 0.0491476 0.0844091 0.116936 0.162039 0.162039 +3 0.160511 0.160511 0.160511 0.160511 0.160511 0.160511 +4 0 0 0 0 0 0 +5 0 0 0 0 0 0 +6 0 0 0 0 0 0 +7 0 0 0 0 0 0 +8 0 0 0 0 0 0 +9 0.676576 0.680769 0.707958 0.709889 0.709889 0.709889 +10 0.697272 0.697272 0.738054 0.738553 0.743446 0.743446 +11 0.754357 0.754357 0.760208 0.760556 0.760556 0.760556 +12 0 0 0 0 0 0 +13 0 0 0 0 0 0 +14 1.00039 1.00039 1.00039 1.0141 1.0141 1.0141 +15 1.01854 1.01854 1.01854 1.01854 1.01854 1.01854 +16 0.970699 0.975675 0.995969 1.04614 1.05545 1.05545 +17 0.992594 1.0202 1.03614 1.08892 1.13746 1.13746 +18 1.09386 1.09386 1.09922 1.10809 1.10809 1.10809 +19 0 0 0 tardis 0 0 +20 0 0 0 0 0 0 +21 0 0 0 0 0 0 +22 1.35506 1.35885 1.36713 1.37285 1.38105 1.38105 +23 1.161 1.18494 1.43935 1.44885 1.46278 1.46278 +24 1.13221 1.20661 1.22248 1.4331 1.45037 1.45037 +25 1.52842 1.52956 1.53387 1.54002 1.54381 1.54381 +26 1.48322 1.49691 1.54058 1.57344 1.60446 1.60675 +27 1.43869 1.51674 1.54557 1.60688 1.6382 1.64727 +28 1.464 1.53106 1.63766 1.68281 1.72392 1.72972 +29 1.61868 1.64211 1.71553 1.75536 1.82599 1.82802 +30 1.64301 1.68357 1.72295 1.79613 1.80546 1.83608 +31 1.69872 1.70717 1.72619 1.73675 1.75281 1.75281 +32 1.7243 1.74704 1.767 1.78202 1.81832 1.86177 +33 1.77673 1.78456 1.79277 1.82968 1.87613 1.88887 +34 1.81019 1.82733 1.86897 1.89782 1.91567 1.91567 +35 0 0 0 0 0 0 +36 0 0 0 0 0 0 +37 0 0 0 0 0 0 +38 0 0 0 0 0 0 +39 0 0 0 0 0 0 +40 0 0 0 0 0 0 +41 0 0 0 0 0 0 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy new file mode 100644 index 00000000000..6a2e6a81a04 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy @@ -0,0 +1,42 @@ +AB000389.1 Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Pseudoalteromonadaceae;Pseudoalteromonas; +AB000699.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB000700.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB000701.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB000702.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB001518.1 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;Flammeovirgaceae;Candidatus_Cardinium; +AB001724.1 Bacteria;Cyanobacteria;SubsectionI;Microcystis; +AB001774.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001775.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001776.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001777.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001779.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001781.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001783.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001784.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001785.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001791.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001793.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001797.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001802.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001805.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001807.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001809.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001813.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001815.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001836.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus; +AB001837.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus; +AB002481.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002483.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002485.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002488.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002489.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002496.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002500.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002504.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002508.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002510.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002512.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002517.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002519.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002523.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002527.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; Tardis diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund new file mode 100644 index 00000000000..c715114a980 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund @@ -0,0 +1,5 @@ +unique 2 94 2 +0.00 2 92 3 +0.01 2 88 5 +0.02 4 84 2 2 1 +0.03 4 75 6 1 2 6 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared new file mode 100644 index 00000000000..ef740a1f151 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared @@ -0,0 +1,3 @@ +label Group numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 +0.10 forest 10 0 5 2 3 1 1 3 3 1 0 +0.10 pasture 10 7 2 5 1 3 2 0 0 1 2 2 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist new file mode 100644 index 00000000000..7c382ecb914 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist @@ -0,0 +1,42 @@ + 98 +U68589 0.000000 0.337144 0.360977 0.415506 0.287299 0.297057 0.392240 0.309315 0.320066 0.328638 0.257245 0.337227 0.301773 0.307105 0.477681 0.364754 0.320363 0.340712 0.643389 0.433138 0.376207 0.351515 0.373270 0.325136 0.289019 0.310340 0.307018 0.308559 0.324956 0.368119 0.324956 0.259707 0.409194 0.273253 0.348793 0.338829 0.289890 0.460196 0.287313 0.304876 0.293627 0.398745 0.323458 0.343931 0.270320 0.328638 0.360667 0.317641 0.307311 0.318242 0.315163 0.334519 0.259354 0.513252 0.321245 0.382122 0.338989 0.311488 0.341095 0.306169 0.343707 0.348475 0.243919 0.301619 0.371532 0.377102 0.428155 0.343582 0.363540 0.320583 0.377095 0.334577 0.328665 0.438795 0.309493 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0.207032 0.304857 0.207984 0.198309 0.307927 0.330148 0.307927 0.270760 0.395785 0.157775 0.310948 0.350243 0.163469 0.426170 0.219999 0.222823 0.236621 0.359680 0.294195 0.329525 0.216845 0.274415 0.339877 0.313301 0.285014 0.308667 0.264831 0.333145 0.301811 0.475087 0.312513 0.319500 0.354966 0.106779 0.320446 0.280287 0.271549 0.376843 0.068529 0.288293 0.341922 0.318118 0.417649 0.334876 0.324266 0.083849 0.375352 0.355032 0.020272 0.438400 0.008059 0.391000 0.333145 0.296162 0.241891 0.328691 0.355843 0.253369 0.268975 0.230455 0.406129 0.072600 0.207438 0.332052 0.009987 0.313227 0.238036 0.418616 0.363081 0.286170 0.372984 0.297339 0.385499 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map new file mode 100644 index 00000000000..51d6458c94b --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map @@ -0,0 +1,18 @@ +0 +0 +0 +7 +0 +0 +4 +10 +13 +8 +0 +0 +9 +0 +0 +0 +0 +0 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos new file mode 100644 index 00000000000..0938450d659 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos @@ -0,0 +1,12 @@ +forward CCGTCAATTCMTTTRAGT +barcode AATGGTAC F003D000 +barcode AACCTGGC F003D002 +barcode TTCGTGGC F003D004 +barcode TTCTTGAC F003D006 +barcode TTCGCGAC F003D008 +barcode TCCAGAAC F003D142 +barcode AAGGCCTC F003D144 +barcode TGACCGTC F003D146 +barcode AGGTTGTC F003D148 +barcode TGGTGAAC F003D150 +barcode AACCGTGTC MOCK.GQY1XT001 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu new file mode 100644 index 00000000000..3b63601d3cd --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu @@ -0,0 +1,37 @@ +label numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 Otu11 Otu12 Otu13 Otu14 Otu15 Otu16 Otu17 Otu18 Otu19 Otu20 Otu21 Otu22 Otu23 Otu24 Otu25 Otu26 Otu27 Otu28 Otu29 Otu30 Otu31 Otu32 Otu33 Otu34 Otu35 Otu36 Otu37 Otu38 Otu39 Otu40 Otu41 Otu42 Otu43 Otu44 Otu45 Otu46 Otu47 Otu48 Otu49 Otu50 Otu51 Otu52 Otu53 Otu54 Otu55 Otu56 Otu57 Otu58 Otu59 Otu60 Otu61 Otu62 Otu63 Otu64 Otu65 Otu66 Otu67 Otu68 Otu69 Otu70 Otu71 Otu72 Otu73 Otu74 Otu75 Otu76 Otu77 Otu78 Otu79 Otu80 Otu81 Otu82 Otu83 Otu84 Otu85 Otu86 Otu87 Otu88 Otu89 Otu90 Otu91 Otu92 Otu93 Otu94 Otu95 Otu96 Otu97 Otu98 +unique 96 U68667,U68641 U68620,U68618 U68663 U68662 U68661 U68660 U68659 U68658 U68657 U68656 U68655 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68688 U68687 U68686 U68685 U68684 U68683 U68682 U68681 U68680 U68679 U68678 U68677 U68676 U68675 U68674 U68673 U68672 U68671 U68670 U68669 U68668 U68666 U68665 U68664 U68613 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68638 U68637 U68636 U68635 U68634 U68633 U68632 U68631 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68615 U68614 +0.01 93 U68688,U68665 U68636,U68631 U68667,U68641 U68620,U68618 U68680,U68615 U68661 U68660 U68659 U68658 U68657 U68656 U68655 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68687 U68686 U68685 U68684 U68683 U68682 U68681 U68679 U68678 U68677 U68676 U68675 U68674 U68673 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68663 U68662 U68613 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68638 U68637 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68614 +0.02 90 U68688,U68665,U68679,U68663 U68673,U68667,U68641 U68636,U68631 U68620,U68618 U68680,U68615 U68658 U68657 U68656 U68655 U68686 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68638 U68687 U68683 U68682 U68681 U68684 U68678 U68677 U68676 U68675 U68674 U68685 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68662 U68661 U68660 U68659 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68637 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68614 U68613 +0.03 88 U68688,U68665,U68679,U68663 U68658,U68638,U68620,U68618 U68673,U68667,U68641 U68636,U68631 U68680,U68615 U68686 U68657 U68656 U68655 U68654 U68653 U68652 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68637 U68687 U68683 U68682 U68681 U68684 U68678 U68677 U68676 U68675 U68674 U68685 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68662 U68661 U68660 U68659 U68613 U68612 U68611 U68610 U68609 U68608 U68607 U68606 U68605 U68603 U68602 U68601 U68600 U68599 U68598 U68597 U68596 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68622 U68621 U68619 U68617 U68616 U68614 +0.04 83 U68688,U68665,U68679,U68663 U68658,U68638,U68620,U68618 U68673,U68667,U68641 U68636,U68631 U68637,U68602 U68652,U68610 U68614,U68596 U68678,U68619 U68680,U68615 U68681,U68677 U68656 U68655 U68654 U68653 U68685 U68651 U68649 U68648 U68647 U68646 U68645 U68644 U68643 U68642 U68640 U68639 U68686 U68687 U68676 U68675 U68674 U68682 U68672 U68671 U68670 U68669 U68668 U68666 U68664 U68662 U68661 U68660 U68683 U68659 U68684 U68657 U68613 U68612 U68611 U68609 U68608 U68607 U68606 U68605 U68603 U68601 U68600 U68599 U68598 U68597 U68595 U68594 U68593 U68592 U68591 U68590 U68589 U68635 U68634 U68633 U68632 U68630 U68629 U68628 U68627 U68626 U68625 U68624 U68623 U68616 U68617 U68622 U68621 +0.05 78 U68688,U68665,U68679,U68663 U68658,U68638,U68620,U68618 U68683,U68652,U68610 U68673,U68667,U68641 U68636,U68631 U68637,U68602 U68628,U68601 U68614,U68596 U68666,U68595 U68672,U68621 U68686,U68635 U68678,U68619 U68680,U68615 U68681,U68677 U68654 U68653 U68651 U68649 U68648 U68647 U68646 U68645 U68685 U68644 U68643 U68642 U68640 U68639 U68687 U68676 U68675 U68674 U68671 U68670 U68669 U68668 U68664 U68662 U68661 U68660 U68682 U68659 U68684 U68657 U68656 U68655 U68607 U68608 U68600 U68609 U68599 U68606 U68598 U68611 U68612 U68613 U68605 U68616 U68617 U68597 U68603 U68594 U68589 U68634 U68590 U68633 U68632 U68591 U68592 U68630 U68629 U68627 U68626 U68625 U68624 U68623 U68622 U68593 +0.06 69 U68688,U68665,U68679,U68663 U68683,U68652,U68610,U68671 U68658,U68638,U68620,U68618 U68673,U68667,U68641,U68598 U68634,U68628,U68601 U68678,U68619,U68645 U68636,U68631 U68633,U68612 U68637,U68602 U68627,U68609 U68648,U68632 U68614,U68596 U68666,U68595 U68605,U68597 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U68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622,U68682,U68657,U68675,U68627,U68609,U68603,U68643,U68664,U68608 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist new file mode 100644 index 00000000000..08b5bb54316 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist @@ -0,0 +1,42 @@ +U68590 U68589 0.337144 +U68591 U68589 0.360977 +U68591 U68590 0.378254 +U68592 U68589 0.415506 +U68592 U68590 0.319757 +U68592 U68591 0.414843 +U68593 U68589 0.287299 +U68593 U68590 0.169021 +U68593 U68591 0.336162 +U68593 U68592 0.284235 +U68594 U68589 0.297057 +U68594 U68590 0.329311 +U68594 U68591 0.356376 +U68594 U68592 0.332574 +U68594 U68593 0.276866 +U68595 U68589 0.39224 +U68595 U68590 0.273158 +U68595 U68591 0.427517 +U68595 U68592 0.229894 +U68595 U68593 0.283055 +U68595 U68594 0.364319 +U68596 U68589 0.309315 +U68596 U68590 0.312653 +U68596 U68591 0.322673 +U68596 U68592 0.36333 +U68596 U68593 0.291774 +U68596 U68594 0.280537 +U68596 U68595 0.360148 +U68597 U68589 0.320066 +U68597 U68590 0.266838 +U68597 U68591 0.35206 +U68597 U68592 0.325227 +U68597 U68593 0.217362 +U68597 U68594 0.263379 +U68597 U68595 0.317196 +U68597 U68596 0.276011 +U68598 U68589 0.328638 +U68598 U68590 0.206259 +U68598 U68591 0.344952 +U68598 U68592 0.265168 +U68598 U68593 0.189372 +U68598 U68594 0.251328 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan new file mode 100644 index 00000000000..0742631b0c9 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan @@ -0,0 +1,42 @@ +#1.36.1 +1 0 0 0 0 0 0 +2 0.049144 0.0491476 0.0844091 0.116936 0.162039 0.162039 +3 0.160511 0.160511 0.160511 0.160511 0.160511 0.160511 +4 0 0 0 0 0 0 +5 0 0 0 0 0 0 +6 0 0 0 0 0 0 +7 0 0 0 0 0 0 +8 0 0 0 0 0 0 +9 0.676576 0.680769 0.707958 0.709889 0.709889 0.709889 +10 0.697272 0.697272 0.738054 0.738553 0.743446 0.743446 +11 0.754357 0.754357 0.760208 0.760556 0.760556 0.760556 +12 0 0 0 0 0 0 +13 0 0 0 0 0 0 +14 1.00039 1.00039 1.00039 1.0141 1.0141 1.0141 +15 1.01854 1.01854 1.01854 1.01854 1.01854 1.01854 +16 0.970699 0.975675 0.995969 1.04614 1.05545 1.05545 +17 0.992594 1.0202 1.03614 1.08892 1.13746 1.13746 +18 1.09386 1.09386 1.09922 1.10809 1.10809 1.10809 +19 0 0 0 0 0 0 +20 0 0 0 0 0 0 +21 0 0 0 0 0 0 +22 1.35506 1.35885 1.36713 1.37285 1.38105 1.38105 +23 1.161 1.18494 1.43935 1.44885 1.46278 1.46278 +24 1.13221 1.20661 1.22248 1.4331 1.45037 1.45037 +25 1.52842 1.52956 1.53387 1.54002 1.54381 1.54381 +26 1.48322 1.49691 1.54058 1.57344 1.60446 1.60675 +27 1.43869 1.51674 1.54557 1.60688 1.6382 1.64727 +28 1.464 1.53106 1.63766 1.68281 1.72392 1.72972 +29 1.61868 1.64211 1.71553 1.75536 1.82599 1.82802 +30 1.64301 1.68357 1.72295 1.79613 1.80546 1.83608 +31 1.69872 1.70717 1.72619 1.73675 1.75281 1.75281 +32 1.7243 1.74704 1.767 1.78202 1.81832 1.86177 +33 1.77673 1.78456 1.79277 1.82968 1.87613 1.88887 +34 1.81019 1.82733 1.86897 1.89782 1.91567 1.91567 +35 0 0 0 0 0 0 +36 0 0 0 0 0 0 +37 0 0 0 0 0 0 +38 0 0 0 0 0 0 +39 0 0 0 0 0 0 +40 0 0 0 0 0 0 +41 0 0 0 0 0 0 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy new file mode 100644 index 00000000000..35dc901458a --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy @@ -0,0 +1,42 @@ +AB000389.1 Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Pseudoalteromonadaceae;Pseudoalteromonas; +AB000699.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB000700.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB000701.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB000702.1 Bacteria;Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; +AB001518.1 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;Flammeovirgaceae;Candidatus_Cardinium; +AB001724.1 Bacteria;Cyanobacteria;SubsectionI;Microcystis; +AB001774.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001775.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001776.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001777.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001779.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001781.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001783.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001784.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001785.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001791.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001793.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001797.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001802.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001805.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001807.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001809.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001813.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001815.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila; +AB001836.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus; +AB001837.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Lactobacillaceae;Lactobacillus; +AB002481.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002483.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002485.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002488.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002489.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002496.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002500.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002504.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002508.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002510.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002512.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002517.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002519.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002523.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; +AB002527.1 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus; diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund new file mode 100644 index 00000000000..47bb1dbaba7 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund @@ -0,0 +1,5 @@ +unique 2 94 2 +0.00 2 92 3 +0.01 2 88 5 +0.02 4 84 2 2 1 +0.03 4 75 6 1 2 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared new file mode 100644 index 00000000000..b119fee3d18 --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared @@ -0,0 +1,3 @@ +label Group numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 +0.10 forest 10 0 5 2 3 1 1 3 3 1 0 +0.10 pasture 10 7 2 5 1 3 2 0 0 1 2 diff --git a/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist new file mode 100644 index 00000000000..298e257b48c --- /dev/null +++ b/lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist @@ -0,0 +1,99 @@ + 98 +U68589 0.000000 0.337144 0.360977 0.415506 0.287299 0.297057 0.392240 0.309315 0.320066 0.328638 0.257245 0.337227 0.301773 0.307105 0.477681 0.364754 0.320363 0.340712 0.643389 0.433138 0.376207 0.351515 0.373270 0.325136 0.289019 0.310340 0.307018 0.308559 0.324956 0.368119 0.324956 0.259707 0.409194 0.273253 0.348793 0.338829 0.289890 0.460196 0.287313 0.304876 0.293627 0.398745 0.323458 0.343931 0.270320 0.328638 0.360667 0.317641 0.307311 0.318242 0.315163 0.334519 0.259354 0.513252 0.321245 0.382122 0.338989 0.311488 0.341095 0.306169 0.343707 0.348475 0.243919 0.301619 0.371532 0.377102 0.428155 0.343582 0.363540 0.320583 0.377095 0.334577 0.328665 0.438795 0.309493 0.394408 0.334519 0.338675 0.228291 0.376110 0.348863 0.282832 0.281554 0.289504 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0.276453 0.191909 0.281513 0.300211 0.286451 0.225078 0.085685 0.333874 0.349992 0.257463 0.093482 0.386847 0.236499 0.218231 0.317777 0.522903 0.364001 0.286170 0.288785 0.211388 0.073795 0.275573 0.310075 0.288419 0.279986 0.079795 0.092710 0.079795 0.275120 0.355097 0.285469 0.134401 0.241633 0.301830 0.371596 0.268092 0.253764 0.282537 0.280475 0.182924 0.159261 0.253005 0.043762 0.259354 0.070985 0.061001 0.229921 0.147447 0.106638 0.294934 0.485847 0.262301 0.096299 0.287010 0.277657 0.198885 0.210837 0.112948 0.297172 0.217019 0.217085 0.103167 0.263548 0.355401 0.087958 0.114629 0.276029 0.355097 0.315321 0.304099 0.414843 0.298075 0.300336 0.106638 0.268562 0.277573 0.330550 0.290224 0.266373 0.087708 0.246819 0.348130 0.257541 0.255902 0.083710 0.291481 0.310785 0.297392 0.347187 0.271852 0.186800 0.296666 0.000000 0.296666 0.297339 +U68687 0.412271 0.313533 0.408262 0.065911 0.357920 0.386580 0.228897 0.367366 0.367276 0.271435 0.389291 0.375794 0.360148 0.262636 0.442034 0.344247 0.334817 0.437586 0.597979 0.406702 0.213348 0.359238 0.388467 0.262900 0.349656 0.403898 0.375748 0.349886 0.281484 0.318118 0.281484 0.387518 0.381696 0.405765 0.309357 0.402710 0.416988 0.403588 0.361088 0.350376 0.406654 0.180258 0.335656 0.301609 0.319116 0.277406 0.160611 0.257463 0.270760 0.374644 0.316294 0.292099 0.371022 0.561599 0.405293 0.325351 0.374436 0.357459 0.354291 0.368248 0.321376 0.230269 0.336101 0.363452 0.311061 0.326299 0.408028 0.311920 0.380934 0.378150 0.391254 0.395909 0.376972 0.489142 0.411804 0.212488 0.292099 0.324272 0.377214 0.374703 0.169254 0.380582 0.233238 0.356923 0.383851 0.351372 0.346968 0.290558 0.419507 0.405876 0.385406 0.383533 0.169021 0.358431 0.118751 0.296666 0.000000 0.385499 +U68688 0.323601 0.316704 0.372984 0.382445 0.336085 0.273784 0.390245 0.221892 0.294195 0.286451 0.291580 0.349854 0.233168 0.302582 0.386206 0.295536 0.274451 0.257572 0.561908 0.435867 0.373578 0.278247 0.350106 0.295676 0.207032 0.304857 0.207984 0.198309 0.307927 0.330148 0.307927 0.270760 0.395785 0.157775 0.310948 0.350243 0.163469 0.426170 0.219999 0.222823 0.236621 0.359680 0.294195 0.329525 0.216845 0.274415 0.339877 0.313301 0.285014 0.308667 0.264831 0.333145 0.301811 0.475087 0.312513 0.319500 0.354966 0.106779 0.320446 0.280287 0.271549 0.376843 0.068529 0.288293 0.341922 0.318118 0.417649 0.334876 0.324266 0.083849 0.375352 0.355032 0.020272 0.438400 0.008059 0.391000 0.333145 0.296162 0.241891 0.328691 0.355843 0.253369 0.268975 0.230455 0.406129 0.072600 0.207438 0.332052 0.009987 0.313227 0.238036 0.418616 0.363081 0.286170 0.372984 0.297339 0.385499 0.000000 From a82a5b20ddd71e1a5180a15220e9aa000f307dbe Mon Sep 17 00:00:00 2001 From: shiltemann Date: Thu, 31 Mar 2016 17:51:25 +0200 Subject: [PATCH 14/18] stylefixes and updates set_metas --- .../ref_to_seq_taxonomy_converter.py | 28 +-- lib/galaxy/datatypes/mothur.py | 187 ++++++++---------- 2 files changed, 95 insertions(+), 120 deletions(-) diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py index 38572b979d0..9394ae0e827 100644 --- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py +++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py @@ -2,30 +2,32 @@ """ convert a ref.taxonommy file to a seq.taxonomy file Usage: -%python ref_to_seq_taxonomy_converter.py +%python ref_to_seq_taxonomy_converter.py """ -import sys, os, re -from math import * +import sys +import re -assert sys.version_info[:2] >= ( 2, 4 ) +assert sys.version_info[:2] >= (2, 4) -def stop_err( msg ): - sys.stderr.write( "%s" % msg ) + +def stop_err(msg): + sys.stderr.write("%s" % msg) sys.exit() + def __main__(): infile_name = sys.argv[1] - outfile = open( sys.argv[2], 'w' ) - pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)]))*(;)?)$' - for i, line in enumerate( file( infile_name ) ): - line = line.rstrip() # eliminate trailing space and new line characters - if not line or line.startswith( '#' ): + outfile = open(sys.argv[2], 'w') + for i, line in enumerate(file(infile_name)): + line = line.rstrip() + if not line or line.startswith('#'): continue fields = line.split('\t') # make sure the 2nd field (taxonomy) ends with a ; - outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$','',fields[1]))) + outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$', '', fields[1]))) outfile.close() -if __name__ == "__main__": __main__() \ No newline at end of file +if __name__ == "__main__": + __main__() diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index a1deb110ff4..0e1145c1cf4 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -26,23 +26,20 @@ class Otu(Text): ncols = 0 data_lines = 0 comment_lines = 0 - try: - with open(dataset.file_name) as fh: - for line in fh: - fields = line.strip().split('\t') - if len(fields) >= 2: - data_lines += 1 - ncols = max(ncols, len(fields)) - label_names.add(fields[0]) - else: - comment_lines += 1 - # Set the discovered metadata values for the dataset - dataset.metadata.data_lines = data_lines - dataset.metadata.columns = ncols - dataset.metadata.labels = list(label_names) - dataset.metadata.labels.sort() - except: - pass + + headers = get_headers(dataset.file_name, sep='\t', count=-1) + for line in headers: + if len(line) >= 2: + data_lines += 1 + ncols = max(ncols, len(line)) + label_names.add(line[0]) + else: + comment_lines += 1 + # Set the discovered metadata values for the dataset + dataset.metadata.data_lines = data_lines + dataset.metadata.columns = ncols + dataset.metadata.labels = list(label_names) + dataset.metadata.labels.sort() def sniff(self, filename): """ @@ -144,35 +141,27 @@ class GroupAbund(Otu): data_lines = 0 comment_lines = 0 ncols = 0 - try: - with open(dataset.file_name) as fh: - line = fh.readline() - fields = line.strip().split('\t') - ncols = max(ncols, len(fields)) - if fields[0] == 'label' and fields[1] == 'Group': - skip = 1 - comment_lines += 1 - else: - skip = 0 - data_lines += 1 - label_names.add(fields[0]) - group_names.add(fields[1]) - for line in fh: - data_lines += 1 - fields = line.strip().split('\t') - ncols = max(ncols, len(fields)) - label_names.add(fields[0]) - group_names.add(fields[1]) - # Set the discovered metadata values for the dataset - dataset.metadata.data_lines = data_lines - dataset.metadata.columns = ncols - dataset.metadata.labels = list(label_names) - dataset.metadata.labels.sort() - dataset.metadata.groups = list(group_names) - dataset.metadata.groups.sort() - dataset.metadata.skip = skip - except: - pass + + headers = get_headers(dataset.file_name, sep='\t', count=max_data_lines) + for line in headers: + if line[0] == 'label' and line[1] == 'Group': + skip = 1 + comment_lines += 1 + else: + skip = 0 + data_lines += 1 + ncols = max(ncols, len(line)) + label_names.add(line[0]) + group_names.add(line[1]) + + # Set the discovered metadata values for the dataset + dataset.metadata.data_lines = data_lines + dataset.metadata.columns = ncols + dataset.metadata.labels = list(label_names) + dataset.metadata.labels.sort() + dataset.metadata.groups = list(group_names) + dataset.metadata.groups.sort() + dataset.metadata.skip = skip def sniff(self, filename, vals_are_int=False): """ @@ -269,14 +258,9 @@ class AlignCheck(Tabular): def set_meta(self, dataset, overwrite=True, **kwd): data_lines = 0 - if dataset.has_data(): - dataset_fh = open(dataset.file_name) - while True: - line = dataset_fh.readline() - if not line: - break - data_lines += 1 - dataset_fh.close() + headers = get_headers(dataset.file_name, sep='\t', count=-1) + for line in headers: + data_lines += 1 dataset.metadata.comment_lines = 1 dataset.metadata.data_lines = data_lines - 1 if data_lines > 0 else 0 dataset.metadata.column_names = self.column_names @@ -309,14 +293,15 @@ class DistanceMatrix(Text): def set_meta(self, dataset, overwrite=True, skip=0, **kwd): Text.set_meta(self, dataset, overwrite=overwrite, skip=skip, **kwd) - try: - with open(dataset.file_name) as fh: - line = '@' - while line[0] == '@': - line = fh.readline().strip().strip() - dataset.metadata.sequence_count = int(line) - except Exception, e: - log.warn("DistanceMatrix set_meta %s" % e) + + headers = get_headers(dataset.file_name, sep='\t', count=-1) + for line in headers: + if not line[0].startswith('@'): + try: + dataset.metadata.sequence_count = int(line[0]) + break + except Exception, e: + log.warn("DistanceMatrix set_meta %s" % e) class LowerTriangleDistanceMatrix(DistanceMatrix): @@ -530,19 +515,15 @@ class Group(Tabular): def set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=None, **kwd): Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines) group_names = set() - try: - with open(dataset.file_name) as fh: - for line in fh: - fields = line.strip().split('\t') - try: - group_names.add(fields[1]) - except IndexError: - # Ignore missing 2nd column - pass - dataset.metadata.groups = [] - dataset.metadata.groups += group_names - except: - pass + + headers = get_headers(dataset.file_name, sep='\t') + for line in headers: + try: + group_names.add(line[1]) + except IndexError: + # Ignore missing 2nd column + pass + dataset.metadata.groups = list(group_names) class AccNos(Tabular): @@ -739,30 +720,23 @@ class CountTable(Tabular): self.column_names = ['name', 'total'] def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd): - try: - data_lines = 0 - with open(dataset.file_name) as fh: - line = fh.readline() - if line: - line = line.strip() - colnames = line.split() - if len(colnames) > 1: - dataset.metadata.columns = len(colnames) - if len(colnames) > 2: - dataset.metadata.groups = colnames[2:] - column_types = ['str'] - for i in range(1, len(colnames)): - column_types.append('int') - dataset.metadata.column_types = column_types - dataset.metadata.comment_lines = 1 - while line: - line = fh.readline() - if not line: - break - data_lines += 1 - dataset.metadata.data_lines = data_lines - except: - pass + + data_lines = 0 + headers = get_headers(dataset.file_name, sep='\t', count=-1) + colnames = headers[0] + if len(colnames) > 1: + dataset.metadata.columns = len(colnames) + if len(colnames) > 2: + dataset.metadata.groups = colnames[2:] + column_types = ['str'] + for i in range(1, len(headers[0])): + column_types.append('int') + dataset.metadata.column_types = column_types + dataset.metadata.comment_lines = 1 + for line in headers[1:]: + data_lines += 1 + + dataset.metadata.data_lines = data_lines class RefTaxonomy(Tabular): @@ -930,12 +904,11 @@ class SffFlow(Tabular): def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd): Tabular.set_meta(self, dataset, overwrite, 1, max_data_lines) + + headers = get_headers(dataset.file_name, sep='\t') try: - with open(dataset.file_name) as fh: - line = fh.readline() - line = line.strip() - flow_values = int(line) - dataset.metadata.flow_values = flow_values + flow_values = int(headers[0][0]) + dataset.metadata.flow_values = flow_values except: pass @@ -947,9 +920,9 @@ class SffFlow(Tabular): out.append('') out.append('%d. Name' % 1) out.append('%d. Flows' % 2) - for i in range(3, dataset.metadata.columns+1): - base = dataset.metadata.flow_order[(i+1) % 4] - out.append('%d. %d %s' % (i-2, base)) + for i in range(3, dataset.metadata.columns + 1): + base = dataset.metadata.flow_order[(i + 1) % 4] + out.append('%d. %d %s' % (i - 2, base)) out.append('') out.append(self.make_html_peek_rows(dataset, skipchars=skipchars)) out.append('') From 3a74c774095c2d3967bba869e74cceaf94479f66 Mon Sep 17 00:00:00 2001 From: shiltemann Date: Thu, 14 Apr 2016 11:51:34 +0200 Subject: [PATCH 15/18] add python optimisations --- .../ref_to_seq_taxonomy_converter.py | 14 +-- lib/galaxy/datatypes/mothur.py | 90 +++++++++---------- 2 files changed, 45 insertions(+), 59 deletions(-) diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py index 9394ae0e827..024731affad 100644 --- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py +++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py @@ -11,21 +11,15 @@ import re assert sys.version_info[:2] >= (2, 4) -def stop_err(msg): - sys.stderr.write("%s" % msg) - sys.exit() - - def __main__(): infile_name = sys.argv[1] outfile = open(sys.argv[2], 'w') for i, line in enumerate(file(infile_name)): line = line.rstrip() - if not line or line.startswith('#'): - continue - fields = line.split('\t') - # make sure the 2nd field (taxonomy) ends with a ; - outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$', '', fields[1]))) + if line and not line.startswith('#'): + fields = line.split('\t') + # make sure the 2nd field (taxonomy) ends with a ; + outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$', '', fields[1]))) outfile.close() diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index 0e1145c1cf4..dc76385e63e 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -298,7 +298,7 @@ class DistanceMatrix(Text): for line in headers: if not line[0].startswith('@'): try: - dataset.metadata.sequence_count = int(line[0]) + dataset.metadata.sequence_count = int(''.join(line)) # seq count sometimes preceded by tab break except Exception, e: log.warn("DistanceMatrix set_meta %s" % e) @@ -518,11 +518,8 @@ class Group(Tabular): headers = get_headers(dataset.file_name, sep='\t') for line in headers: - try: + if len(line) > 1: group_names.add(line[1]) - except IndexError: - # Ignore missing 2nd column - pass dataset.metadata.groups = list(group_names) @@ -556,10 +553,10 @@ class Oligos(Text): count = 0 for line in headers: if not line[0].startswith('@') and not line[0].startswith('#'): - if len(line) == 2 and re.match('forward|reverse', line[0]): + if len(line) == 2 and line[0] in ['forward', 'reverse']: count += 1 continue - elif len(line) == 3 and re.match('barcode', line[0]): + elif len(line) == 3 and line[0] == 'barcode': count += 1 continue else: @@ -720,22 +717,18 @@ class CountTable(Tabular): self.column_names = ['name', 'total'] def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd): - data_lines = 0 headers = get_headers(dataset.file_name, sep='\t', count=-1) colnames = headers[0] + dataset.metadata.column_types = ['str'] + (['int'] * ( len(headers[0]) - 1)) if len(colnames) > 1: dataset.metadata.columns = len(colnames) if len(colnames) > 2: dataset.metadata.groups = colnames[2:] - column_types = ['str'] - for i in range(1, len(headers[0])): - column_types.append('int') - dataset.metadata.column_types = column_types - dataset.metadata.comment_lines = 1 for line in headers[1:]: data_lines += 1 + dataset.metadata.comment_lines = 1 dataset.metadata.data_lines = data_lines @@ -774,15 +767,15 @@ class RefTaxonomy(Tabular): """ headers = get_headers(filename, sep='\t', count=300) count = 0 - pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$' + pat_prog = re.compile('^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?)*(;)?)$') found_semicolons = False for line in headers: if not line[0].startswith('@') and not line[0].startswith('#'): if not (2 <= len(line) <= 3): return False - if not re.match(pat, line[1]): + if not pat_prog.match(line[1]): return False - if not found_semicolons and str(line[1]).count(';') > 0: + if not found_semicolons and line[1].find(';') > -1: found_semicolons = True if len(line) == 3: try: @@ -852,28 +845,27 @@ class Axes(Tabular): col_cnt = None all_integers = True for line in headers: - if count == 0: - pass - elif col_cnt is None: - col_cnt = len(line) - if col_cnt < 2: - return False - else: - if len(line) != col_cnt: - return False - try: - for i in range(1, col_cnt): - check = float(line[i]) - # Check abs value is <= 1.0 - if abs(check) > 1.0: - return False - # Also test for whether value is an integer - try: - check = int(line[i]) - except ValueError: - all_integers = False - except ValueError: - return False + if count != 0: + if col_cnt is None: + col_cnt = len(line) + if col_cnt < 2: + return False + else: + if len(line) != col_cnt: + return False + try: + for i in range(1, col_cnt): + check = float(line[i]) + # Check abs value is <= 1.0 + if abs(check) > 1.0: + return False + # Also test for whether value is an integer + try: + check = int(line[i]) + except ValueError: + all_integers = False + except ValueError: + return False count += 1 if count > 0: @@ -909,24 +901,24 @@ class SffFlow(Tabular): try: flow_values = int(headers[0][0]) dataset.metadata.flow_values = flow_values - except: - pass + except Exception, e: + log.warn("SffFlow set_meta %s" % e) def make_html_table(self, dataset, skipchars=[]): """Create HTML table, used for displaying peek""" - out = [''] try: + out = '
' + # Generate column header - out.append('') - out.append('' % 1) - out.append('' % 2) + out += '' + out += '' % 1 + out += '' % 2 for i in range(3, dataset.metadata.columns + 1): base = dataset.metadata.flow_order[(i + 1) % 4] - out.append('' % (i - 2, base)) - out.append('') - out.append(self.make_html_peek_rows(dataset, skipchars=skipchars)) - out.append('
%d. Name%d. Flows
%d. Name%d. Flows%d. %d %s
') - out = "".join(out) + out += '%d. %d %s' % (i - 2, base) + out += '' + out += self.make_html_peek_rows(dataset, skipchars=skipchars) + out += '' except Exception, exc: out = "Can't create peek %s" % str(exc) return out From f56e81a996511869f4a068418ffcd104c1b0ccdc Mon Sep 17 00:00:00 2001 From: shiltemann Date: Thu, 21 Apr 2016 16:34:55 +0200 Subject: [PATCH 16/18] allow for comment lines in Otu files --- lib/galaxy/datatypes/mothur.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index dc76385e63e..05312449a91 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -29,7 +29,7 @@ class Otu(Text): headers = get_headers(dataset.file_name, sep='\t', count=-1) for line in headers: - if len(line) >= 2: + if len(line) >= 2 and not line[0].startswith('@'): data_lines += 1 ncols = max(ncols, len(line)) label_names.add(line[0]) From d47f8f577e358b4e7a71b15a905040e5d3b079d4 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 27 Apr 2016 09:14:54 -0400 Subject: [PATCH 17/18] Fixup exception handling in mothur datatypes. --- lib/galaxy/datatypes/mothur.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/datatypes/mothur.py b/lib/galaxy/datatypes/mothur.py index 05312449a91..a17a5f07cba 100644 --- a/lib/galaxy/datatypes/mothur.py +++ b/lib/galaxy/datatypes/mothur.py @@ -300,7 +300,7 @@ class DistanceMatrix(Text): try: dataset.metadata.sequence_count = int(''.join(line)) # seq count sometimes preceded by tab break - except Exception, e: + except Exception as e: log.warn("DistanceMatrix set_meta %s" % e) @@ -608,7 +608,7 @@ class Frequency(Tabular): try: int(line[0]) float(line[1]) - except: + except Exception: return False count += 1 if count > 1: @@ -658,7 +658,7 @@ class Quantile(Tabular): float(line[4]) float(line[5]) float(line[6]) - except: + except Exception: return False count += 1 if count > 0: @@ -780,7 +780,7 @@ class RefTaxonomy(Tabular): if len(line) == 3: try: int(line[2]) - except: + except Exception: return False count += 1 @@ -901,7 +901,7 @@ class SffFlow(Tabular): try: flow_values = int(headers[0][0]) dataset.metadata.flow_values = flow_values - except Exception, e: + except Exception as e: log.warn("SffFlow set_meta %s" % e) def make_html_table(self, dataset, skipchars=[]): @@ -919,7 +919,7 @@ class SffFlow(Tabular): out += '' out += self.make_html_peek_rows(dataset, skipchars=skipchars) out += '' - except Exception, exc: + except Exception as exc: out = "Can't create peek %s" % str(exc) return out From d73a86d3658ed2ff7815ba5bd57ae63e527d4381 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 27 Apr 2016 09:15:05 -0400 Subject: [PATCH 18/18] Add a sample sniff test for new Mothur datatype. The existing sniffer tests with the mothur stuff tests the sniffers in isolation - this is more of an integration test that tests the sample datatype configuration for the newly added mothur stuff. --- lib/galaxy/datatypes/sniff.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py index ff9584d8b47..3e8b8e04c02 100644 --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -343,6 +343,9 @@ def guess_ext( fname, sniff_order, is_multi_byte=False ): >>> fname = get_test_fname('5e5z.pdb') >>> guess_ext(fname, sniff_order) 'pdb' + >>> fname = get_test_fname('mothur_datatypetest_true.mothur.otu') + >>> guess_ext(fname, sniff_order) + 'mothur.otu' """ for datatype in sniff_order: """