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comparison gops_coverage.py @ 2:bc9c66c1e9c9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:48:05 -0500
parents 1e864693a1c0
children 4ef9819dc7fb
comparison
equal deleted inserted replaced
1:16b62a897aac 2:bc9c66c1e9c9
5 5
6 usage: %prog bed_file_1 bed_file_2 out_file 6 usage: %prog bed_file_1 bed_file_2 out_file
7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file 7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file 8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
9 """ 9 """
10 import sys, traceback, fileinput 10 import fileinput
11 from warnings import warn 11 import sys
12 from bx.intervals import * 12 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
13 from bx.intervals.io import * 13 from bx.intervals.operations.coverage import coverage
14 from bx.intervals.operations.coverage import *
15 from bx.cookbook import doc_optparse 14 from bx.cookbook import doc_optparse
16 from galaxy.tools.util.galaxyops import * 15 from bx.tabular.io import ParseError
16 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
17 17
18 assert sys.version_info[:2] >= ( 2, 4 ) 18 assert sys.version_info[:2] >= ( 2, 4 )
19 19
20
20 def main(): 21 def main():
21 upstream_pad = 0
22 downstream_pad = 0
23
24 options, args = doc_optparse.parse( __doc__ ) 22 options, args = doc_optparse.parse( __doc__ )
25 try: 23 try:
26 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) 24 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
27 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) 25 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
28 in_fname, in2_fname, out_fname = args 26 in_fname, in2_fname, out_fname = args
29 except: 27 except:
30 doc_optparse.exception() 28 doc_optparse.exception()
31 29
32 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), 30 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
43 fix_strand=True ) 41 fix_strand=True )
44 42
45 out_file = open( out_fname, "w" ) 43 out_file = open( out_fname, "w" )
46 44
47 try: 45 try:
48 for line in coverage( [g1,g2] ): 46 for line in coverage( [g1, g2] ):
49 if type( line ) is GenomicInterval: 47 if type( line ) is GenomicInterval:
50 out_file.write( "%s\n" % "\t".join( line.fields ) ) 48 out_file.write( "%s\n" % "\t".join( line.fields ) )
51 else: 49 else:
52 out_file.write( "%s\n" % line ) 50 out_file.write( "%s\n" % line )
53 except ParseError, exc: 51 except ParseError, exc: