Mercurial > repos > xuebing > sharplabtool
comparison tools/new_operations/gops_basecoverage.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 Count total base coverage. | |
| 4 | |
| 5 usage: %prog in_file out_file | |
| 6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file | |
| 7 """ | |
| 8 from galaxy import eggs | |
| 9 import pkg_resources | |
| 10 pkg_resources.require( "bx-python" ) | |
| 11 import sys, traceback, fileinput | |
| 12 from warnings import warn | |
| 13 from bx.intervals import * | |
| 14 from bx.intervals.io import * | |
| 15 from bx.intervals.operations.base_coverage import * | |
| 16 from bx.cookbook import doc_optparse | |
| 17 from galaxy.tools.util.galaxyops import * | |
| 18 | |
| 19 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 20 | |
| 21 def main(): | |
| 22 upstream_pad = 0 | |
| 23 downstream_pad = 0 | |
| 24 | |
| 25 options, args = doc_optparse.parse( __doc__ ) | |
| 26 try: | |
| 27 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
| 28 in_fname, out_fname = args | |
| 29 except: | |
| 30 doc_optparse.exception() | |
| 31 | |
| 32 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), | |
| 33 chrom_col=chr_col_1, | |
| 34 start_col=start_col_1, | |
| 35 end_col=end_col_1, | |
| 36 strand_col = strand_col_1, | |
| 37 fix_strand=True ) | |
| 38 | |
| 39 try: | |
| 40 bases = base_coverage(g1) | |
| 41 except ParseError, exc: | |
| 42 fail( "Invalid file format: %s" % str( exc ) ) | |
| 43 out_file = open( out_fname, "w" ) | |
| 44 out_file.write( "%s\n" % str( bases ) ) | |
| 45 out_file.close() | |
| 46 if g1.skipped > 0: | |
| 47 print skipped( g1, filedesc="" ) | |
| 48 | |
| 49 if __name__ == "__main__": | |
| 50 main() |