Mercurial > repos > devteam > basecoverage
diff gops_basecoverage.py @ 5:37652c34b3bf draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author | devteam |
---|---|
date | Thu, 22 Jun 2017 18:37:49 -0400 |
parents | c929b6540d07 |
children | 4d584cf5ced5 |
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--- a/gops_basecoverage.py Fri Dec 18 19:36:36 2015 -0500 +++ b/gops_basecoverage.py Thu Jun 22 18:37:49 2017 -0400 @@ -5,12 +5,14 @@ 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.cookbook import doc_optparse from bx.tabular.io import ParseError from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped @@ -34,13 +36,14 @@ try: bases = base_coverage(g1) - except ParseError, exc: + 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="" ) + print(skipped( g1, filedesc="" )) + if __name__ == "__main__": main()