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(1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool.

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This commit is contained in:
Jeremy Goecks
2011-08-14 19:49:26 -04:00
parent 29bc117ac1
commit 08cfd112cd
2 changed files with 62 additions and 29 deletions
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lib/galaxy/datatypes/util/gff_util.py
+11
View File
@@ -87,6 +87,13 @@ class GFFFeature( GFFInterval ):
intervals_copy.append( interval.copy() )
return GFFFeature(self.reader, self.chrom_col, self.feature_col, self.start_col, self.end_col, self.strand_col,
self.score_col, self.strand, intervals=intervals_copy )
def lines( self ):
lines = []
for interval in self.intervals:
lines.append( '\t'.join( interval.fields ) )
return lines
class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ):
"""
@@ -209,6 +216,10 @@ class GFFReaderWrapper( NiceReaderWrapper ):
#finally:
#raw_size += len( self.current_line )
# Ignore comments.
if isinstance( interval, Comment ):
continue
# If interval not associated with feature, break.
group = interval.attributes.get( 'group', None )
# GFF test:
tools/extract/extract_genomic_dna.py
+51 -29
View File
@@ -14,6 +14,7 @@ import pkg_resources
pkg_resources.require( "bx-python" )
import sys, string, os, re, tempfile, subprocess
from bx.cookbook import doc_optparse
from bx.intervals.io import Header, Comment
import bx.seq.nib
import bx.seq.twobit
from galaxy.tools.util.galaxyops import *
@@ -111,9 +112,17 @@ def __main__():
#
# Fetch sequences.
#
# Get feature's line(s).
def get_lines( feature ):
if isinstance( feature, gff_util.GFFFeature ):
return feature.lines()
else:
return [ feature.rstrip( '\r\n' ) ]
skipped_lines = 0
first_invalid_line = 0
invalid_line = ''
invalid_lines = []
fout = open( output_filename, "w" )
warnings = []
warning = ''
@@ -121,7 +130,13 @@ def __main__():
file_iterator = open( input_filename )
if gff_format and interpret_features:
file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False )
for i, feature in enumerate( file_iterator ):
line_count = 1
for feature in file_iterator:
# Ignore comments, headers.
if isinstance( feature, ( Header, Comment ) ):
line_count += 1
continue
if gff_format and interpret_features:
# Processing features.
gff_util.convert_gff_coords_to_bed( feature )
@@ -145,18 +160,18 @@ def __main__():
except:
warning = "Invalid chrom, start or end column values. "
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if start > end:
warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if strand not in ['+', '-']:
@@ -174,13 +189,13 @@ def __main__():
nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) )
try:
sequence = nib.get( start, end-start )
except:
except Exception, e:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
elif seq_path and os.path.isfile( seq_path ):
if not(twobitfile):
@@ -194,29 +209,29 @@ def __main__():
else:
sequence = twobitfile[chrom][start:end]
except:
warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " %( start, end-start, chrom )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
else:
warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if sequence == '':
warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " \
% ( chrom, start, end, dbkey )
warnings.append( warning )
skipped_lines += 1
if not invalid_line:
first_invalid_line = i + 1
invalid_line = line
if not invalid_lines:
invalid_lines = get_lines( feature )
first_invalid_line = line_count
skipped_lines += len( invalid_lines )
continue
if includes_strand_col and strand == "-":
sequence = reverse_complement( sequence )
@@ -248,6 +263,12 @@ def __main__():
else:
format_str = "%s\t%s\n"
fout.write( format_str % ( meta_data, str( sequence ) ) )
# Update line count.
if isinstance( feature, gff_util.GFFFeature ):
line_count += len( feature.intervals )
else:
line_count += 1
fout.close()
@@ -256,6 +277,7 @@ def __main__():
warn_msg += warnings[0]
print warn_msg
if skipped_lines:
print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
# Error message includes up to the first 10 skipped lines.
print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) )
if __name__ == "__main__": __main__()