view gops_basecoverage.py @ 6:9c5ff4695c97 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c

#!/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

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


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 Exception:
        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()