1 | #!/usr/bin/env python |
---|
2 | |
---|
3 | #FIXME: THIS IS 1:1 COPY OF THE SAME FUNCTIONED TOOL - ALLOW REGULAR TOOLS TO MASCARADE AS CONVERTERS |
---|
4 | |
---|
5 | """ |
---|
6 | Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. |
---|
7 | |
---|
8 | usage: %prog input output shift |
---|
9 | """ |
---|
10 | |
---|
11 | import sys, shutil, os |
---|
12 | from galaxy import eggs |
---|
13 | import pkg_resources |
---|
14 | pkg_resources.require( "GeneTrack" ) |
---|
15 | |
---|
16 | from genetrack.scripts import tabs2genetrack |
---|
17 | from genetrack import logger |
---|
18 | |
---|
19 | if __name__ == "__main__": |
---|
20 | import os |
---|
21 | os.environ[ 'LC_ALL' ] = 'C' |
---|
22 | #os.system( 'export' ) |
---|
23 | |
---|
24 | parser = tabs2genetrack.option_parser() |
---|
25 | |
---|
26 | options, args = parser.parse_args() |
---|
27 | |
---|
28 | # uppercase the format |
---|
29 | options.format = options.format.upper() |
---|
30 | |
---|
31 | if options.format not in ('BED', 'GFF'): |
---|
32 | sys.stdout = sys.stderr |
---|
33 | parser.print_help() |
---|
34 | sys.exit(-1) |
---|
35 | |
---|
36 | logger.disable(options.verbosity) |
---|
37 | |
---|
38 | # missing file names |
---|
39 | if not (options.inpname and options.outname and options.format): |
---|
40 | parser.print_help() |
---|
41 | sys.exit(-1) |
---|
42 | else: |
---|
43 | tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ |
---|
44 | format=options.format, shift=options.shift, index=options.index, options=options) |
---|