mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
69 lines
2.3 KiB
Python
69 lines
2.3 KiB
Python
#!/usr/bin/env python
|
|
"""
|
|
Calculate coverage of one query on another, and append the coverage to
|
|
the last two columns as bases covered and percent coverage.
|
|
|
|
usage: %prog bed_file_1 bed_file_2 out_file
|
|
-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
|
|
-2, --cols2=N,N,N,N: Columns for start, end, strand in second file
|
|
"""
|
|
from galaxy import eggs
|
|
import pkg_resources
|
|
pkg_resources.require( "bx-python" )
|
|
import sys, traceback, fileinput
|
|
from warnings import warn
|
|
from bx.intervals import *
|
|
from bx.intervals.io import *
|
|
from bx.intervals.operations.coverage import *
|
|
from bx.cookbook import doc_optparse
|
|
from galaxy.tools.util.galaxyops import *
|
|
|
|
assert sys.version_info[:2] >= ( 2, 4 )
|
|
|
|
def main():
|
|
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 )
|
|
chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
|
|
in_fname, in2_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 )
|
|
g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
|
|
chrom_col=chr_col_2,
|
|
start_col=start_col_2,
|
|
end_col=end_col_2,
|
|
strand_col=strand_col_2,
|
|
fix_strand=True )
|
|
|
|
out_file = open( out_fname, "w" )
|
|
|
|
try:
|
|
for line in coverage( [g1,g2] ):
|
|
if type( line ) is GenomicInterval:
|
|
out_file.write( "%s\n" % "\t".join( line.fields ) )
|
|
else:
|
|
out_file.write( "%s\n" % line )
|
|
except ParseError, exc:
|
|
out_file.close()
|
|
fail( "Invalid file format: %s" % str( exc ) )
|
|
|
|
out_file.close()
|
|
|
|
if g1.skipped > 0:
|
|
print skipped( g1, filedesc=" of 1st dataset" )
|
|
if g2.skipped > 0:
|
|
print skipped( g2, filedesc=" of 2nd dataset" )
|
|
|
|
if __name__ == "__main__":
|
|
main()
|