comparison gops_basecoverage.py @ 5:37652c34b3bf draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

4:346e0034714a

Count total base coverage.

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

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

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

                            strand_col=strand_col_1,
                            fix_strand=True )

    try:
        bases = base_coverage(g1)
    except ParseError, 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()

5:37652c34b3bf

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 )

                            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()