Mercurial > repos > charles-bernard > alfa
changeset 31:7df7bee710ad draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Sun, 18 Dec 2016 09:50:39 -0500 |
| parents | 1c9cea51dc24 |
| children | b26aec436ab5 |
| files | ALFA/ALFA_wrapper.py |
| diffstat | 1 files changed, 7 insertions(+), 6 deletions(-) [+] |
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--- a/ALFA/ALFA_wrapper.py Sun Dec 18 09:33:46 2016 -0500 +++ b/ALFA/ALFA_wrapper.py Sun Dec 18 09:50:39 2016 -0500 @@ -60,10 +60,11 @@ reads_labels = [''] * (n/2) for i in range(0, n, 2): reads_filenames[k] = reads_list[i].split('__fname__')[1] - reads_labels[k] = reads_list[i+1].split('__label__')[1] + cur_label = reads_list[i+1].split('__label__')[1] + reads_labels[k] = re.sub(r' ', '_', cur_label) if not reads_labels[k]: reads_labels[k] = 'sample_%s' % str(k) - input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k]) + input2_args='%s "%s" "%s"' % (input2_args, reads_filenames[k], reads_labels[k]) k += 1 if format == 'bedgraph': input2_args = input2_args + ' --bedgraph' @@ -85,7 +86,7 @@ def merge_count_files(reads_labels): merged_count_file = open('count_file.txt', 'wb') for i in range(0, len(reads_labels)): - current_count_file = open(reads_labels[i] + '.categories_counts', 'r') + current_count_file = open('%s.categories_counts' % reads_labels[i], 'r') merged_count_file.write('##LABEL: %s\n\n' % reads_labels[i]) merged_count_file.write(current_count_file.read()) merged_count_file.write('__________________________________________________________________\n') @@ -106,11 +107,11 @@ 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 = symlink_user_indexes(args.indexes[0], args.indexes[1]) - input1_args = '-g %s' % index + input1_args = '-g "%s"' % index elif args.bi_indexes: - input1_args = '-g %s' % args.bi_indexes[0] + input1_args = '-g "%s"' % args.bi_indexes[0] elif args.annotation_file: - input1_args = '-a %s' % args.annotation_file[0] + input1_args = '-a "%s"' % args.annotation_file[0] else: exit_and_explain('No annotation file submitted !')