Mercurial > repos > charles-bernard > alfa
changeset 28:2496883e588b draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Fri, 04 Nov 2016 06:12:07 -0400 |
| parents | c3f91012ac19 |
| children | c8acc8808b52 |
| files | ALFA/ALFA_wrapper.py |
| diffstat | 1 files changed, 6 insertions(+), 7 deletions(-) [+] |
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--- a/ALFA/ALFA_wrapper.py Fri Nov 04 06:11:49 2016 -0400 +++ b/ALFA/ALFA_wrapper.py Fri Nov 04 06:12:07 2016 -0400 @@ -44,10 +44,12 @@ args = parser.parse_args() return args -def mv_and_rename_user_indexes(stranded_index, unstranded_index): +def symlink_user_indexes(stranded_index, unstranded_index): index='index' - shutil.copy(stranded_index, index + '.stranded.index') - shutil.copy(unstranded_index, index + '.unstranded.index') + os.symlink(stranded_index, index + '.stranded.index') + os.symlink(unstranded_index, index + '.unstranded.index') + #shutil.copy(stranded_index, index + '.stranded.index') + #shutil.copy(unstranded_index, index + '.unstranded.index') return index def get_input2_args(reads_list, format): @@ -99,17 +101,14 @@ if not (args.output_pdf or args.output_png or args.output_svg or args.output_indexes or args.output_count): exit_and_explain('Error: no output to return\nProcess Aborted\n') - tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='') - logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s') - alfa_path = os.path.join(args.GALAXY_TOOL_DIR[0], 'ALFA.py') #INPUT1: Annotation File if args.indexes: # The indexes submitted by the user must exhibit the suffix '.(un)stranded.index' and will be called by alfa by their prefix - index = mv_and_rename_user_indexes(args.indexes[0], args.indexes[1]) + index = symlink_user_indexes(args.indexes[0], args.indexes[1]) input1_args = '-g %s' % index elif args.bi_indexes: input1_args = '-g %s' % args.bi_indexes[0]