Mercurial > repos > devteam > complement
view gops_complement.py @ 2:a3c7fd2ae338
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author | Dave Bouvier <dave@bx.psu.edu> |
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date | Mon, 14 Apr 2014 12:33:32 -0400 |
parents | b4415197029e |
children | 48d2f6a56a90 |
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#!/usr/bin/env python """ Complement regions. usage: %prog in_file out_file -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file -l, --lengths=N: Filename of .len file for species (chromosome lengths) -a, --all: Complement all chromosomes (Genome-wide complement) """ import sys, traceback, fileinput from warnings import warn from bx.intervals import * from bx.intervals.io import * from bx.intervals.operations.complement import complement from bx.intervals.operations.subtract import subtract from bx.cookbook import doc_optparse from galaxy.tools.util.galaxyops import * assert sys.version_info[:2] >= ( 2, 4 ) def main(): allchroms = False upstream_pad = 0 downstream_pad = 0 options, args = doc_optparse.parse( __doc__ ) try: chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) lengths = options.lengths if options.all: allchroms = True in_fname, out_fname = args except: doc_optparse.exception() g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), chrom_col=chr_col_1, start_col=start_col_1, end_col=end_col_1, strand_col=strand_col_1, fix_strand=True ) lens = dict() chroms = list() # dbfile is used to determine the length of each chromosome. The lengths # are added to the lens dict and passed copmlement operation code in bx. dbfile = fileinput.FileInput( lengths ) if dbfile: if not allchroms: try: for line in dbfile: fields = line.split("\t") lens[fields[0]] = int(fields[1]) except: # assume LEN doesn't exist or is corrupt somehow pass elif allchroms: try: for line in dbfile: fields = line.split("\t") end = int(fields[1]) chroms.append("\t".join([fields[0],"0",str(end)])) except: pass # Safety...if the dbfile didn't exist and we're on allchroms, then # default to generic complement if allchroms and len(chroms) == 0: allchroms = False if allchroms: chromReader = GenomicIntervalReader(chroms) generator = subtract([chromReader, g1]) else: generator = complement(g1, lens) out_file = open( out_fname, "w" ) try: for interval in generator: if type( interval ) is GenomicInterval: out_file.write( "%s\n" % "\t".join( interval ) ) else: out_file.write( "%s\n" % interval ) except ParseError, exc: out_file.close() fail( "Invalid file format: %s" % str( exc ) ) out_file.close() if g1.skipped > 0: print skipped( g1, filedesc="" ) if __name__ == "__main__": main()