annotate gops_basecoverage.py @ 5:21898544368b draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9

#!/usr/bin/env python
"""
Count total base coverage.

usage: %prog in_file out_file
    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
"""
from __future__ import print_function

import fileinput
import sys

from bx.cookbook import doc_optparse
from bx.intervals.io import NiceReaderWrapper
from bx.intervals.operations.base_coverage import base_coverage
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped

assert sys.version_info[:2] >= ( 2, 4 )


def main():
    options, args = doc_optparse.parse( __doc__ )
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
        in_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 )

    try:
        bases = base_coverage(g1)
    except ParseError as exc:
        fail( "Invalid file format: %s" % str( exc ) )
    out_file = open( out_fname, "w" )
    out_file.write( "%s\n" % str( bases ) )
    out_file.close()
    if g1.skipped > 0:
        print(skipped( g1, filedesc="" ))


if __name__ == "__main__":
    main()