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.
73 lines
2.2 KiB
Python
73 lines
2.2 KiB
Python
#!/usr/bin/env python
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"""
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Calculate coverage of one query on another, and append the coverage to
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the last two columns as bases covered and percent coverage.
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usage: %prog bed_file_1 bed_file_2 out_file
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-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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-2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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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.coverage import *
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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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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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chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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in_fname, in2_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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g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
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chrom_col=chr_col_2,
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start_col=start_col_2,
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end_col=end_col_2,
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strand_col=strand_col_2,
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fix_strand=True)
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out_file = open( out_fname, "w" )
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try:
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for line in coverage([g1,g2]):
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if type( line ) is GenomicInterval:
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print >> out_file, "\t".join( line.fields )
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else:
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print >> out_file, line
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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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print skipped( g1, filedesc=" of 1st dataset" )
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if g2.skipped > 0:
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print skipped( g2, filedesc=" of 2nd dataset" )
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if __name__ == "__main__":
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main()
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