Mercurial > repos > xuebing > sharplabtool
comparison tools/new_operations/gops_coverage.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #!/usr/bin/env python | |
| 2 """ | |
| 3 Calculate coverage of one query on another, and append the coverage to | |
| 4 the last two columns as bases covered and percent coverage. | |
| 5 | |
| 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 | |
| 8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file | |
| 9 """ | |
| 10 from galaxy import eggs | |
| 11 import pkg_resources | |
| 12 pkg_resources.require( "bx-python" ) | |
| 13 import sys, traceback, fileinput | |
| 14 from warnings import warn | |
| 15 from bx.intervals import * | |
| 16 from bx.intervals.io import * | |
| 17 from bx.intervals.operations.coverage import * | |
| 18 from bx.cookbook import doc_optparse | |
| 19 from galaxy.tools.util.galaxyops import * | |
| 20 | |
| 21 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 22 | |
| 23 def main(): | |
| 24 upstream_pad = 0 | |
| 25 downstream_pad = 0 | |
| 26 | |
| 27 options, args = doc_optparse.parse( __doc__ ) | |
| 28 try: | |
| 29 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
| 30 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) | |
| 31 in_fname, in2_fname, out_fname = args | |
| 32 except: | |
| 33 doc_optparse.exception() | |
| 34 | |
| 35 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), | |
| 36 chrom_col=chr_col_1, | |
| 37 start_col=start_col_1, | |
| 38 end_col=end_col_1, | |
| 39 strand_col=strand_col_1, | |
| 40 fix_strand=True ) | |
| 41 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ), | |
| 42 chrom_col=chr_col_2, | |
| 43 start_col=start_col_2, | |
| 44 end_col=end_col_2, | |
| 45 strand_col=strand_col_2, | |
| 46 fix_strand=True ) | |
| 47 | |
| 48 out_file = open( out_fname, "w" ) | |
| 49 | |
| 50 try: | |
| 51 for line in coverage( [g1,g2] ): | |
| 52 if type( line ) is GenomicInterval: | |
| 53 out_file.write( "%s\n" % "\t".join( line.fields ) ) | |
| 54 else: | |
| 55 out_file.write( "%s\n" % line ) | |
| 56 except ParseError, exc: | |
| 57 out_file.close() | |
| 58 fail( "Invalid file format: %s" % str( exc ) ) | |
| 59 | |
| 60 out_file.close() | |
| 61 | |
| 62 if g1.skipped > 0: | |
| 63 print skipped( g1, filedesc=" of 1st dataset" ) | |
| 64 if g2.skipped > 0: | |
| 65 print skipped( g2, filedesc=" of 2nd dataset" ) | |
| 66 | |
| 67 if __name__ == "__main__": | |
| 68 main() |