[2] | 1 | #!/usr/bin/env python |
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| 2 | """ |
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| 3 | Count total base coverage. |
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| 4 | |
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| 5 | usage: %prog in_file out_file |
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| 6 | -1, --cols1=N,N,N,N: Columns for start, end, strand in first file |
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| 7 | """ |
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| 8 | from galaxy import eggs |
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| 9 | import pkg_resources |
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| 10 | pkg_resources.require( "bx-python" ) |
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| 11 | import sys, traceback, fileinput |
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| 12 | from warnings import warn |
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| 13 | from bx.intervals import * |
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| 14 | from bx.intervals.io import * |
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| 15 | from bx.intervals.operations.base_coverage import * |
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| 16 | from bx.cookbook import doc_optparse |
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| 17 | from galaxy.tools.util.galaxyops import * |
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| 18 | |
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| 19 | assert sys.version_info[:2] >= ( 2, 4 ) |
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| 20 | |
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| 21 | def main(): |
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| 22 | upstream_pad = 0 |
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| 23 | downstream_pad = 0 |
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| 24 | |
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| 25 | options, args = doc_optparse.parse( __doc__ ) |
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| 26 | try: |
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| 27 | chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) |
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| 28 | in_fname, out_fname = args |
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| 29 | except: |
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| 30 | doc_optparse.exception() |
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| 31 | |
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| 32 | g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), |
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| 33 | chrom_col=chr_col_1, |
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| 34 | start_col=start_col_1, |
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| 35 | end_col=end_col_1, |
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| 36 | strand_col = strand_col_1, |
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| 37 | fix_strand=True ) |
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| 38 | |
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| 39 | try: |
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| 40 | bases = base_coverage(g1) |
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| 41 | except ParseError, exc: |
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| 42 | fail( "Invalid file format: %s" % str( exc ) ) |
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| 43 | out_file = open( out_fname, "w" ) |
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| 44 | out_file.write( "%s\n" % str( bases ) ) |
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| 45 | out_file.close() |
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| 46 | if g1.skipped > 0: |
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| 47 | print skipped( g1, filedesc="" ) |
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| 48 | |
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| 49 | if __name__ == "__main__": |
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| 50 | main() |
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