mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
Nate Coraor
7560751dc8
Whether running locally or via PBS, $PATH should now be handled in your user's environment. This also fixes problems like PYTHONPATH on the new blast nodes being wrong (because they are x86_64 and the frontends are i686). Note that you can actually start Galaxy without having an eggs dir now.
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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-d, --db=N: Database name (for determining 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
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import traceback
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import 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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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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db = options.db
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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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out_file = open( out_fname, "w" )
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lens = dict()
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chroms = list()
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dbfile = fileinput.FileInput( "static/ucsc/chrom/"+db+".len" )
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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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try:
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for interval in generator:
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if type( interval ) is GenomicInterval:
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print >> out_file, "\t".join( interval )
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else:
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print >> out_file, interval
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except ParseError, exc:
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print >> sys.stderr, "Invalid file format: ", str( exc )
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if g1.skipped > 0:
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first_line, line_contents = g1.skipped_lines[0]
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print 'Condition/data issue: skipped %d invalid lines starting at line #%d which is "%s"' % ( g1.skipped, first_line, line_contents )
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if __name__ == "__main__":
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main()
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