Mercurial > repos > charles-bernard > alfa
comparison ALFA/ALFA_wrapper.py @ 29:c8acc8808b52 draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Sat, 19 Nov 2016 04:25:42 -0500 |
| parents | 2496883e588b |
| children | 1c9cea51dc24 |
comparison
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| 28:2496883e588b | 29:c8acc8808b52 |
|---|---|
| 46 | 46 |
| 47 def symlink_user_indexes(stranded_index, unstranded_index): | 47 def symlink_user_indexes(stranded_index, unstranded_index): |
| 48 index='index' | 48 index='index' |
| 49 os.symlink(stranded_index, index + '.stranded.index') | 49 os.symlink(stranded_index, index + '.stranded.index') |
| 50 os.symlink(unstranded_index, index + '.unstranded.index') | 50 os.symlink(unstranded_index, index + '.unstranded.index') |
| 51 #shutil.copy(stranded_index, index + '.stranded.index') | |
| 52 #shutil.copy(unstranded_index, index + '.unstranded.index') | |
| 53 return index | 51 return index |
| 54 | 52 |
| 55 def get_input2_args(reads_list, format): | 53 def get_input2_args(reads_list, format): |
| 56 n = len(reads_list) | 54 n = len(reads_list) |
| 57 if n%2 != 0: | 55 if n%2 != 0: |
| 58 exit_and_explain('Problem with pairing reads filename and reads label') | 56 exit_and_explain('Problem with pairing reads filename and reads label') |
| 59 input2_args='-i' | 57 input2_args='-i' |
| 60 k = 0 | 58 k = 1 |
| 61 reads_filenames = [''] * (n/2) | 59 reads_filenames = [''] * (n/2) |
| 62 reads_labels = [''] * (n/2) | 60 reads_labels = [''] * (n/2) |
| 63 for i in range(0, n, 2): | 61 for i in range(0, n, 2): |
| 64 reads_filenames[k] = reads_list[i].split('__fname__')[1] | 62 reads_filenames[k] = reads_list[i].split('__fname__')[1] |
| 65 reads_labels[k] = reads_list[i+1].split('__label__')[1] | 63 reads_labels[k] = reads_list[i+1].split('__label__')[1] |
| 66 if not reads_labels[k]: | 64 if not reads_labels[k]: |
| 67 reads_labels[k] = 'sample_%s' % str(k+1) | 65 reads_labels[k] = 'sample_%s' % str(k) |
| 68 input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k]) | 66 input2_args='%s %s %s' % (input2_args, reads_filenames[k], reads_labels[k]) |
| 69 k += 1 | 67 k += 1 |
| 70 if format == 'bedgraph': | 68 if format == 'bedgraph': |
| 71 input2_args = input2_args + ' --bedgraph' | 69 input2_args = input2_args + ' --bedgraph' |
| 72 return input2_args, reads_filenames, reads_labels | 70 return input2_args, reads_filenames, reads_labels |
| 86 | 84 |
| 87 def merge_count_files(reads_labels): | 85 def merge_count_files(reads_labels): |
| 88 merged_count_file = open('count_file.txt', 'wb') | 86 merged_count_file = open('count_file.txt', 'wb') |
| 89 for i in range(0, len(reads_labels)): | 87 for i in range(0, len(reads_labels)): |
| 90 current_count_file = open(reads_labels[i] + '.categories_counts', 'r') | 88 current_count_file = open(reads_labels[i] + '.categories_counts', 'r') |
| 91 reads_label = reads_labels[i] | 89 merged_count_file.write('##LABEL: %s\n\n' % reads_label[i]) |
| 92 merged_count_file.write('##LABEL: %s\n\n' % reads_label) | |
| 93 merged_count_file.write(current_count_file.read()) | 90 merged_count_file.write(current_count_file.read()) |
| 94 merged_count_file.write('__________________________________________________________________\n') | 91 merged_count_file.write('__________________________________________________________________\n') |
| 95 current_count_file.close() | 92 current_count_file.close() |
| 96 merged_count_file.close() | 93 merged_count_file.close() |
| 97 return 'count_file.txt' | 94 return 'count_file.txt' |