Mercurial > repos > charles-bernard > alfa
diff ALFA/ALFA_wrapper.py @ 29:c8acc8808b52 draft
Uploaded
author | charles-bernard |
---|---|
date | Sat, 19 Nov 2016 04:25:42 -0500 |
parents | 2496883e588b |
children | 1c9cea51dc24 |
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--- a/ALFA/ALFA_wrapper.py Fri Nov 04 06:12:07 2016 -0400 +++ b/ALFA/ALFA_wrapper.py Sat Nov 19 04:25:42 2016 -0500 @@ -48,8 +48,6 @@ index='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): @@ -57,14 +55,14 @@ if n%2 != 0: exit_and_explain('Problem with pairing reads filename and reads label') input2_args='-i' - k = 0 + k = 1 reads_filenames = [''] * (n/2) 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] if not reads_labels[k]: - reads_labels[k] = 'sample_%s' % str(k+1) + reads_labels[k] = 'sample_%s' % str(k) input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k]) k += 1 if format == 'bedgraph': @@ -88,8 +86,7 @@ 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') - reads_label = reads_labels[i] - merged_count_file.write('##LABEL: %s\n\n' % reads_label) + merged_count_file.write('##LABEL: %s\n\n' % reads_label[i]) merged_count_file.write(current_count_file.read()) merged_count_file.write('__________________________________________________________________\n') current_count_file.close() @@ -180,4 +177,4 @@ shutil.move(args.bi_indexes[1] + '.unstranded.index', args.output_index[1]) cleanup_before_exit(tmp_dir) -main() \ No newline at end of file +main()