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https://github.com/galaxyproject/galaxy.git
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Daniel Blankenberg
86f0862aa4
Cron scripts on test and main will need to be updated when the server is. GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
99 lines
3.0 KiB
Python
99 lines
3.0 KiB
Python
#!/usr/bin/env python
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"""
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Complement regions.
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usage: %prog in_file out_file
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-1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
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-l, --lengths=N: Filename of .len file for species (chromosome lengths)
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-a, --all: Complement all chromosomes (Genome-wide complement)
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"""
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import sys, traceback, fileinput
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from warnings import warn
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from bx.intervals import *
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from bx.intervals.io import *
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from bx.intervals.operations.complement import complement
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from bx.intervals.operations.subtract import subtract
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from bx.cookbook import doc_optparse
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from galaxy.tools.util.galaxyops import *
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assert sys.version_info[:2] >= ( 2, 4 )
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def main():
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allchroms = False
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upstream_pad = 0
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downstream_pad = 0
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options, args = doc_optparse.parse( __doc__ )
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try:
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chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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lengths = options.lengths
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if options.all: allchroms = True
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in_fname, out_fname = args
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except:
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doc_optparse.exception()
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g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
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chrom_col=chr_col_1,
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start_col=start_col_1,
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end_col=end_col_1,
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strand_col=strand_col_1,
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fix_strand=True )
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lens = dict()
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chroms = list()
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# dbfile is used to determine the length of each chromosome. The lengths
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# are added to the lens dict and passed copmlement operation code in bx.
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dbfile = fileinput.FileInput( lengths )
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if dbfile:
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if not allchroms:
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try:
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for line in dbfile:
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fields = line.split("\t")
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lens[fields[0]] = int(fields[1])
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except:
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# assume LEN doesn't exist or is corrupt somehow
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pass
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elif allchroms:
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try:
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for line in dbfile:
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fields = line.split("\t")
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end = int(fields[1])
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chroms.append("\t".join([fields[0],"0",str(end)]))
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except:
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pass
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# Safety...if the dbfile didn't exist and we're on allchroms, then
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# default to generic complement
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if allchroms and len(chroms) == 0:
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allchroms = False
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if allchroms:
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chromReader = GenomicIntervalReader(chroms)
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generator = subtract([chromReader, g1])
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else:
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generator = complement(g1, lens)
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out_file = open( out_fname, "w" )
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try:
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for interval in generator:
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if type( interval ) is GenomicInterval:
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out_file.write( "%s\n" % "\t".join( interval ) )
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else:
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out_file.write( "%s\n" % interval )
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except ParseError, exc:
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out_file.close()
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fail( "Invalid file format: %s" % str( exc ) )
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out_file.close()
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if g1.skipped > 0:
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print skipped( g1, filedesc="" )
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if __name__ == "__main__":
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main()
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