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https://github.com/galaxyproject/galaxy.git
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Add a new metadata type of Metadata Files.
These are now used to store the list of chromosomes for species as well as the index for MAF files. MAF tools have been enhanced to make use of index files when available. TODO: When datasets are purged from disk, these files should also be purged.
This commit is contained in:
Daniel Blankenberg
@@ -9,7 +9,6 @@ log = logging.getLogger(__name__)
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# Valid first column and strand column values vor bed, other formats
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col1_startswith = ['chr', 'chl', 'groupun', 'reftig_', 'scaffold', 'super_', 'vcho']
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valid_strand = ['+', '-', '.']
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gzip_magic = '\037\213'
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class DataMeta( type ):
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"""
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@@ -86,10 +85,19 @@ class Data( object ):
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def set_readonly_meta( self, dataset ):
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"""Unimplemented method, resets the readonly metadata values"""
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return True
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def missing_meta( self, dataset ):
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"""Checks for empty metadata values, Returns True if non-optional metadata is missing"""
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for key, value in dataset.metadata.items():
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if dataset.metadata.spec[key].get("optional"): continue #we skip check for optional values here
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def missing_meta( self, dataset, check = [], skip = [] ):
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"""
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Checks for empty metadata values, Returns True if non-optional metadata is missing
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Specifying a list of 'check' values will only check those names provided; when used, optionality is ignored
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Specifying a list of 'skip' items will return True even when a named metadata value is missing
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"""
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if check:
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to_check = [ ( to_check, dataset.metadata.get( to_check ) ) for to_check in check ]
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else:
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to_check = dataset.metadata.items()
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for key, value in to_check:
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if key in skip or ( not check and dataset.metadata.spec[key].get( "optional" ) ):
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continue #we skip check for optional and nonrequested values here
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if not value:
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return True
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return False
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@@ -328,7 +336,7 @@ def get_file_peek( file_name, WIDTH=256, LINE_COUNT=5 ):
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line = line[ :WIDTH ]
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if not data_checked and line:
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data_checked = True
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if line[0:2] == gzip_magic:
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if line[0:2] == util.gzip_magic:
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file_type = 'gzipped'
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break
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else:
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@@ -1,8 +1,9 @@
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import sys, logging
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import sys, logging, copy, shutil
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from galaxy.util import string_as_bool
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from galaxy.util.odict import odict
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from galaxy.web import form_builder
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import galaxy.model
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log = logging.getLogger( __name__ )
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@@ -75,7 +76,13 @@ class MetadataCollection:
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def get_html_by_name( self, name, **kwd ):
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if name in self.spec:
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return self.spec[name].param.get_html( value=getattr( self, name ), context=self, **kwd )
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def make_dict_copy( self, to_copy ):
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"""Makes a deep copy of input iterable to_copy according to self.spec"""
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rval = {}
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for key, value in to_copy.items():
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if key in self.spec:
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rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy )
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return rval
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class MetadataSpecCollection( odict ):
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"""
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@@ -121,7 +128,10 @@ class MetadataParameter( object ):
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def to_string( self, value ):
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return str( value )
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def make_copy( self, value, target_context = None, source_context = None ):
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return copy.deepcopy( value )
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@classmethod
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def marshal ( cls, value ):
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"""
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@@ -151,7 +161,6 @@ class MetadataParameter( object ):
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"""
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return value
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class MetadataElementSpec( object ):
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"""
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Defines a metadata element and adds it to the metadata_spec (which
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@@ -280,16 +289,14 @@ class ColumnTypesParameter( MetadataParameter ):
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return ",".join( map( str, value ) )
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class PythonObjectParameter( MetadataParameter ):
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def __init__( self, spec ):
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MetadataParameter.__init__( self, spec )
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def to_string( self, value ):
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if not value:
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return self.spec.to_string( self.spec.no_value )
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return self.spec.to_string( value )
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return self.spec._to_string( self.spec.no_value )
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return self.spec._to_string( value )
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def get_html_field( self, value=None, context={}, other_values={}, **kwd ):
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return form_builder.TextField( self.spec.name, value=self.to_string( value ) )
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return form_builder.TextField( self.spec.name, value=self._to_string( value ) )
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def get_html( self, value=None, context={}, other_values={}, **kwd ):
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return str( self )
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@@ -297,3 +304,40 @@ class PythonObjectParameter( MetadataParameter ):
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@classmethod
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def marshal( cls, value ):
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return value
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class FileParameter( MetadataParameter ):
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def to_string( self, value ):
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if not value:
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return str( self.spec.no_value )
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return value.file_name
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def get_html_field( self, value=None, context={}, other_values={}, **kwd ):
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return form_builder.TextField( self.spec.name, value=str( value.id ) )
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def get_html( self, value=None, context={}, other_values={}, **kwd ):
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return "<div>No display available for Metadata Files</div>"
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def wrap( self, value ):
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if isinstance( value, galaxy.model.MetadataFile ):
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return value
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try:
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return galaxy.model.MetadataFile.get( value )
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except:
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#value was not a valid id
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return None
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def make_copy( self, value, target_context = None, source_context = None ):
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value = self.wrap( value )
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if value:
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new_value = galaxy.model.MetadataFile( dataset = target_context.parent, name = self.spec.name )
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new_value.flush()
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shutil.copy( value.file_name, new_value.file_name )
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return self.unwrap( new_value )
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return None
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@classmethod
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def marshal( cls, value ):
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if isinstance( value, galaxy.model.MetadataFile ):
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value = value.id
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return value
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@@ -8,6 +8,7 @@ import re
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from cgi import escape
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from galaxy.datatypes.metadata import MetadataElement
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from galaxy.datatypes import metadata
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import galaxy.model
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from galaxy import util
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from sniff import *
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@@ -24,7 +25,6 @@ class Alignment( Sequence ):
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"""Add metadata elements"""
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MetadataElement( name="species", desc="Species", default=[], param=metadata.SelectParameter, multiple=True, readonly=True, no_value=None )
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MetadataElement( name="species_chromosomes", desc="Species Chromosomes", value={}, param=metadata.PythonObjectParameter, readonly=True, no_value={}, to_string=str, visible=False )
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class Fasta( Sequence ):
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"""Class representing a FASTA sequence"""
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@@ -192,23 +192,30 @@ except:
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class Maf( Alignment ):
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"""Class describing a Maf alignment"""
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file_ext = "maf"
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#Readonly and optional, users can't unset it, but if it is not set, we are generally ok; if required use a metadata validator in the tool definition
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MetadataElement( name="species_chromosomes", desc="Species Chromosomes", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True )
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MetadataElement( name="maf_index", desc="MAF Index File", param=metadata.FileParameter, readonly=True, no_value=None, visible=False, optional=True )
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def init_meta( self, dataset, copy_from=None ):
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Alignment.init_meta( self, dataset, copy_from=copy_from )
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def set_meta( self, dataset, overwrite = True, **kwd ):
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"""
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Parses and sets species and chromosomes from MAF files.
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Parses and sets species, chromosomes, index from MAF file.
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"""
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#these metadata values are not accessable by users, always overwrite
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species = []
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species_chromosomes = {}
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maf_reader = bx.align.maf.Reader( open( dataset.file_name ) )
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indexes = bx.interval_index_file.Indexes()
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try:
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for i, m in enumerate( bx.align.maf.Reader( open(dataset.file_name) ) ):
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for c in m.components:
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## spec,chrom = bx.align.maf.src_split( c.src )
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## if not spec or not chrom: spec = chrom = c.src
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# "src_split" finds the rightmost dot, which is probably
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# wrong in general, and certainly here.
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while True:
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pos = maf_reader.file.tell()
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block = maf_reader.next()
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if block is None: break
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for c in block.components:
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spec = c.src
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chrom = None
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if "." in spec:
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@@ -218,20 +225,44 @@ class Maf( Alignment ):
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species_chromosomes[spec] = []
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if chrom and chrom not in species_chromosomes[spec]:
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species_chromosomes[spec].append( chrom )
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# only check first 100,000 blocks for species
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if i > 100000: break
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except:
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indexes.add( c.src, c.forward_strand_start, c.forward_strand_end, pos, max=c.src_size )
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except: #bad MAF file
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pass
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#these metadata values are not accessable by users, always overwrite
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dataset.metadata.species = species
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dataset.metadata.species_chromosomes = species_chromosomes
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#only overwrite the contents if our newly determined chromosomes don't match stored
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chrom_file = dataset.metadata.species_chromosomes
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compare_chroms = {}
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if chrom_file:
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try:
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for line in open( chrom_file.file_name ):
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fields = line.split( "\t" )
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if fields:
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spec = fields.pop( 0 )
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if spec:
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compare_chroms[spec] = fields
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except:
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pass
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#write out species chromosomes again only if values are different
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if not species_chromosomes or compare_chroms != species_chromosomes:
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tmp_file = tempfile.TemporaryFile( 'w+b' )
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for spec, chroms in species_chromosomes.items():
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tmp_file.write( "%s\t%s\n" % ( spec, "\t".join( chroms ) ) )
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if not chrom_file:
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chrom_file = galaxy.model.MetadataFile( dataset = dataset, name = "species_chromosomes" )
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chrom_file.flush()
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tmp_file.seek( 0 )
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open( chrom_file.file_name, 'wb' ).write( tmp_file.read() )
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dataset.metadata.species_chromosomes = chrom_file
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tmp_file.close()
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index_file = dataset.metadata.maf_index
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if not index_file:
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index_file = galaxy.model.MetadataFile( dataset = dataset, name="maf_index" )
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index_file.flush()
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indexes.write( open( index_file.file_name, 'w' ) )
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dataset.metadata.maf_index = index_file
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def missing_meta( self, dataset ):
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"""Checks to see if species is set"""
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if dataset.metadata.species in [None, []]:
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return True
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return False
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def display_peek( self, dataset ):
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"""Returns formated html of peek"""
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return self.make_html_table( dataset )
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@@ -475,7 +475,16 @@ class JobWrapper( object ):
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def get_input_fnames( self ):
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job = model.Job.get( self.job_id )
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return [ da.dataset.file_name for da in job.input_datasets if da.dataset ]
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filenames = []
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for da in job.input_datasets: #da is JobToInputDatasetAssociation object
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if da.dataset:
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filenames.append( da.dataset.file_name )
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#we will need to stage in metadata file names also
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#TODO: would be better to only stage in metadata files that are actually needed (found in command line, referenced in config files, etc.)
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for key, value in da.dataset.metadata.items():
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if isinstance( value, model.MetadataFile ):
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filenames.append( value.file_name )
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return filenames
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def get_output_fnames( self ):
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job = model.Job.get( self.job_id )
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@@ -5,7 +5,7 @@ Naming: try to use class names that have a distinct plural form so that
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the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
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"""
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import os.path, os, errno, copy
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import os.path, os, errno
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import sha
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import galaxy.datatypes
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from galaxy.util.bunch import Bunch
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@@ -165,7 +165,7 @@ class HistoryDatasetAssociation( object ):
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return self._metadata_collection
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def set_metadata( self, bunch ):
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# Needs to accept a MetadataCollection, a bunch, or a dict
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self._metadata = dict( [ ( key, copy.deepcopy( value ) ) for key, value in bunch.items() ] )
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self._metadata = self.metadata.make_dict_copy( bunch )
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metadata = property( get_metadata, set_metadata )
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"""
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@@ -223,8 +223,8 @@ class HistoryDatasetAssociation( object ):
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return self.datatype.set_meta( self, **kwd )
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def set_readonly_meta( self, **kwd ):
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return self.datatype.set_readonly_meta( self, **kwd )
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def missing_meta( self ):
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return self.datatype.missing_meta( self )
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def missing_meta( self, **kwd ):
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return self.datatype.missing_meta( self, **kwd )
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def as_display_type( self, type, **kwd ):
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return self.datatype.as_display_type( self, type, **kwd )
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def display_peek( self ):
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@@ -258,8 +258,9 @@ class HistoryDatasetAssociation( object ):
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return self.datatype.find_conversion_destination( self, accepted_formats, datatypes_registry, **kwd )
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def copy( self, copy_children = False, parent_id = None ):
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des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self )
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des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self )
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des.flush()
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des.metadata = self.metadata #need to set after flushed, as MetadataFiles require dataset.id
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if copy_children:
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for child in self.children:
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child_copy = child.copy( copy_children = copy_children, parent_id = des.id )
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@@ -564,6 +565,24 @@ class StoredWorkflowMenuEntry( object ):
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self.user = None
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self.order_index = None
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class MetadataFile( object ):
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def __init__( self, dataset = None, name = None ):
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self.dataset = dataset
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self.name = name
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@property
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def file_name( self ):
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assert self.id is not None, "ID must be set before filename used (commit the object)"
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path = os.path.join( Dataset.file_path, '_metadata_files', *directory_hash_id( self.id ) )
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# Create directory if it does not exist
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try:
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os.makedirs( path )
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except OSError, e:
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# File Exists is okay, otherwise reraise
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if e.errno != errno.EEXIST:
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raise
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# Return filename inside hashed directory
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return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) )
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## ---- Utility methods -------------------------------------------------------
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def directory_hash_id( id ):
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@@ -238,6 +238,15 @@ StoredWorkflowMenuEntry.table = Table( "stored_workflow_menu_entry", metadata,
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Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
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Column( "order_index", Integer ) )
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MetadataFile.table = Table( "metadata_file", metadata,
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Column( "id", Integer, primary_key=True ),
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Column( "name", String ),
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Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ),
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Column( "create_time", DateTime, default=now ),
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Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
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Column( "deleted", Boolean, index=True, default=False ),
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Column( "purged", Boolean, index=True, default=False ) )
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# With the tables defined we can define the mappers and setup the
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# relationships between the model objects.
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@@ -363,6 +372,9 @@ assign_mapper( context, StoredWorkflowUserShareAssociation, StoredWorkflowUserSh
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assign_mapper( context, StoredWorkflowMenuEntry, StoredWorkflowMenuEntry.table,
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properties=dict( stored_workflow=relation( StoredWorkflow ) ) )
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assign_mapper( context, MetadataFile, MetadataFile.table,
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properties=dict( dataset=relation( HistoryDatasetAssociation ) ) )
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def db_next_hid( self ):
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"""
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Override __next_hid to generate from the database in a concurrency
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@@ -196,7 +196,7 @@ class UploadToolAction( object ):
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temp = open( temp_name, "U" )
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magic_check = temp.read( 2 )
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temp.close()
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if magic_check != datatypes.data.gzip_magic:
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if magic_check != util.gzip_magic:
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return ( False, False )
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CHUNK_SIZE = 2**15 # 32Kb
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gzipped_file = gzip.GzipFile( temp_name )
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@@ -60,4 +60,4 @@ def params_from_strings( params, param_values, app, ignore_errors=False ):
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if key in params:
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value = params[key].value_from_basic( value, app, ignore_errors )
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rval[ key ] = value
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return rval
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return rval
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@@ -829,6 +829,8 @@ class DrillDownSelectToolParameter( ToolParameter ):
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options = []
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for filter_key, filter_value in self.filtered.iteritems():
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dataset = other_values[filter_key]
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if dataset.__class__.__name__.endswith( "DatasetFilenameWrapper" ): #this is a bad way to check for this, but problems importing class ( due to circular imports? )
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dataset = dataset.dataset
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if dataset:
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for meta_key, meta_dict in filter_value.iteritems():
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if dataset.metadata.spec[meta_key].param.to_string( dataset.metadata.get( meta_key ) ) == meta_dict['value']:
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@@ -163,13 +163,15 @@ class MetadataValidator( Validator ):
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"""
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Validator that checks for missing metadata
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"""
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def __init__( self, message=None ):
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def __init__( self, message = None, check = "", skip = "" ):
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self.message = message
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self.check = check.split( "," )
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self.skip = skip.split( "," )
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@classmethod
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def from_element( cls, param, elem ):
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return cls( elem.get( 'message', None ) )
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return cls( message=elem.get( 'message', None ), check=elem.get( 'check', "" ), skip=elem.get( 'skip', "" ) )
|
||||
def validate( self, value, history=None ):
|
||||
if value and value.missing_meta():
|
||||
if value and value.missing_meta( check = self.check, skip = self.skip ):
|
||||
if self.message is None:
|
||||
self.message = "Metadata missing, click the pencil icon in the history item to edit / save the metadata attributes"
|
||||
raise ValueError( self.message )
|
||||
|
||||
@@ -145,8 +145,16 @@ def maf_index_by_uid( maf_uid, index_location_file ):
|
||||
except:
|
||||
pass
|
||||
return None
|
||||
|
||||
#return ( index, temp_index_filename ) for user maf, if available, or build one and return it, return None when no tempfile is created
|
||||
def open_or_build_maf_index( maf_file, index_filename, species = None ):
|
||||
try:
|
||||
return ( bx.align.maf.Indexed( maf_file, index_filename = index_filename, keep_open = True, parse_e_rows = False ), None )
|
||||
except:
|
||||
return build_maf_index( maf_file, species = species )
|
||||
|
||||
|
||||
#builds and returns (index, index_filename) for specified maf_file
|
||||
#builds and returns ( index, index_filename ) for specified maf_file
|
||||
def build_maf_index( maf_file, species = None ):
|
||||
indexes = bx.interval_index_file.Indexes()
|
||||
try:
|
||||
|
||||
@@ -17,6 +17,8 @@ from elementtree import ElementTree
|
||||
log = logging.getLogger(__name__)
|
||||
_lock = threading.RLock()
|
||||
|
||||
gzip_magic = '\037\213'
|
||||
|
||||
def synchronized(func):
|
||||
"""This wrapper will serialize access to 'func' to a single thread. Use it as a decorator."""
|
||||
def caller(*params, **kparams):
|
||||
|
||||
@@ -65,6 +65,9 @@
|
||||
if they are not accurate.
|
||||
</div>
|
||||
</form>
|
||||
%if data.missing_meta():
|
||||
<div class="errormessagesmall">Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.</div>
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
@@ -2,7 +2,8 @@
|
||||
#Retreives data from UCSC and stores in a file. UCSC parameters are provided in the input/output file.
|
||||
import urllib, sys, os, gzip, tempfile, shutil
|
||||
from galaxy import eggs
|
||||
from galaxy.datatypes import data
|
||||
#from galaxy.datatypes import data
|
||||
from galaxy.util import gzip_magic
|
||||
|
||||
assert sys.version_info[:2] >= ( 2, 4 )
|
||||
|
||||
@@ -14,7 +15,7 @@ def check_gzip( filename ):
|
||||
temp = open( filename, "U" )
|
||||
magic_check = temp.read( 2 )
|
||||
temp.close()
|
||||
if magic_check != data.gzip_magic:
|
||||
if magic_check != gzip_magic:
|
||||
return False
|
||||
return True
|
||||
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
<tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks">
|
||||
<description>given a set of coding exon intervals</description>
|
||||
<command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
|
||||
<command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
|
||||
#else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
|
||||
#end if
|
||||
</command>
|
||||
|
||||
@@ -16,6 +16,7 @@ usage: %prog maf_file [options]
|
||||
-S, --strandCol=S: Column of Strand
|
||||
-t, --mafType=t: Type of MAF source to use
|
||||
-m, --mafFile=m: Path of source MAF file, if not using cached version
|
||||
-I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
|
||||
-i, --interval_file=i: Input interval file
|
||||
-o, --output_file=o: Output MAF file
|
||||
-p, --species=p: Species to include in output
|
||||
@@ -92,7 +93,7 @@ def __main__():
|
||||
print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( options.mafType )
|
||||
sys.exit()
|
||||
elif options.mafFile:
|
||||
index, index_filename = maf_utilities.build_maf_index( options.mafFile, species = [dbkey] )
|
||||
index, index_filename = maf_utilities.open_or_build_maf_index( options.mafFile, options.mafIndex, species = [dbkey] )
|
||||
if index is None:
|
||||
print >> sys.stderr, "Your MAF file appears to be malformed."
|
||||
sys.exit()
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
<tool id="Interval2Maf1" name="Extract MAF blocks">
|
||||
<description>given a set of genomic intervals</description>
|
||||
<command interpreter="python">
|
||||
#if $maf_source_type.maf_source == "user":#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc
|
||||
#if $maf_source_type.maf_source == "user":#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc
|
||||
#else:#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc
|
||||
#end if
|
||||
</command>
|
||||
|
||||
@@ -15,6 +15,7 @@ usage: %prog maf_file [options]
|
||||
-G, --geneBED: Input is a Gene BED file, process and join exons as one region
|
||||
-t, --mafSourceType=t: Type of MAF source to use
|
||||
-m, --mafSource=m: Path of source MAF file, if not using cached version
|
||||
-I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
|
||||
-i, --interval_file=i: Input interval file
|
||||
-o, --output_file=o: Output MAF file
|
||||
-p, --species=p: Species to include in output
|
||||
@@ -105,7 +106,7 @@ def __main__():
|
||||
stop_err( "The MAF source specified (%s) appears to be invalid." % ( options.mafSource ) )
|
||||
elif options.mafSourceType.lower() in ["user"]:
|
||||
#index maf for use here, need to remove index_file when finished
|
||||
index, index_filename = maf_utilities.build_maf_index( options.mafSource, species = [primary_species] )
|
||||
index, index_filename = maf_utilities.open_or_build_maf_index( options.mafSource, options.mafIndex, species = [primary_species] )
|
||||
if index is None:
|
||||
stop_err( "Your MAF file appears to be malformed." )
|
||||
else:
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks">
|
||||
<description>given a set of genomic intervals</description>
|
||||
<command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
|
||||
<command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
|
||||
#else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
|
||||
#end if
|
||||
</command>
|
||||
|
||||
@@ -31,10 +31,14 @@ def __main__():
|
||||
else: summary = False
|
||||
|
||||
mafIndexFile = "%s/maf_index.loc" % sys.argv[9]
|
||||
try:
|
||||
maf_index_filename = sys.argv[10].strip()
|
||||
except:
|
||||
maf_index_filename = None
|
||||
index = index_filename = None
|
||||
if maf_source_type == "user":
|
||||
#index maf for use here
|
||||
index, index_filename = maf_utilities.build_maf_index( input_maf_filename, species = [dbkey] )
|
||||
index, index_filename = maf_utilities.open_or_build_maf_index( input_maf_filename, maf_index_filename, species = [dbkey] )
|
||||
if index is None:
|
||||
print >>sys.stderr, "Your MAF file appears to be malformed."
|
||||
sys.exit()
|
||||
|
||||
@@ -7,7 +7,10 @@
|
||||
#else:
|
||||
$maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
|
||||
#end if
|
||||
${GALAXY_DATA_INDEX_DIR}
|
||||
${GALAXY_DATA_INDEX_DIR}
|
||||
#if $maf_source_type.maf_source == "user":
|
||||
$input2.metadata.maf_index
|
||||
#end if
|
||||
</command>
|
||||
<inputs>
|
||||
<param format="interval" name="input1" label="Interval File" type="data">
|
||||
|
||||
@@ -4,7 +4,6 @@
|
||||
|
||||
import sys, sets, re, os.path
|
||||
from galaxy import eggs
|
||||
from galaxy.datatypes import metadata
|
||||
|
||||
assert sys.version_info[:2] >= ( 2, 4 )
|
||||
|
||||
|
||||
@@ -2,7 +2,9 @@
|
||||
<description>Multiple Alignment Viewer</description>
|
||||
<command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command>
|
||||
<inputs>
|
||||
<param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/>
|
||||
<param name="maf_input" type="data" format="maf" label="Alignment File" optional="False">
|
||||
<validator type="metadata" check="species_chromosomes" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
|
||||
</param>
|
||||
<param name="refseq" label="Reference Sequence" type="select">
|
||||
<option value="first" selected="true">First sequence in each block</option>
|
||||
<option value="any">Any sequence</option>
|
||||
@@ -103,9 +105,19 @@ nowarn = $nowarn
|
||||
|
||||
#set $seq_count = 0
|
||||
#for $annotation_count, $annotation in $enumerate( $annotations ):
|
||||
#if $annotation.annotation_style.style == "galaxy":
|
||||
#if $maf_input.dataset.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.dataset.metadata.species_chromosomes and $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]:
|
||||
#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.dataset.metadata.species_chromosomes[$annotation.annotation_style['species'].value]]
|
||||
#if $annotation.annotation_style.style == "galaxy":
|
||||
#set $species_chromosomes = {}
|
||||
#if $maf_input.dataset.metadata.species_chromosomes:
|
||||
#for $line in open( $maf_input.dataset.metadata.species_chromosomes.file_name ):
|
||||
#set $fields = $line.split( "\t" )
|
||||
#if $fields:
|
||||
#set $spec = $fields.pop( 0 )
|
||||
#set $species_chromosomes[spec] = $fields
|
||||
#end if
|
||||
#end for
|
||||
#end if
|
||||
#if $species_chromosomes and $annotation.annotation_style['species'].value in $species_chromosomes and $species_chromosomes[$annotation.annotation_style['species'].value]:
|
||||
#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $species_chromosomes[$annotation.annotation_style['species'].value]]
|
||||
#else:
|
||||
#set $seq_names = [$annotation.annotation_style['species']]
|
||||
#end if
|
||||
@@ -171,4 +183,4 @@ For detailed information on GMAJ, click here_.
|
||||
Gmaj is a tool for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by programs such as TBA (though it can also be used with maf-format alignments from other sources). It can display interactive graphical and text representations of the alignments, a diagram showing the locations of exons and repeats, and other annotations -- all with the user's choice of reference sequence.
|
||||
|
||||
</help>
|
||||
</tool>
|
||||
</tool>
|
||||
|
||||
Reference in New Issue
Block a user