Mercurial > repos > charles-bernard > alfa
comparison ALFA/ALFA_wrapper.py @ 32:b26aec436ab5 draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Thu, 21 Dec 2017 09:29:26 -0500 |
| parents | 7df7bee710ad |
| children |
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| 31:7df7bee710ad | 32:b26aec436ab5 |
|---|---|
| 52 | 52 |
| 53 def get_input2_args(reads_list, format): | 53 def get_input2_args(reads_list, format): |
| 54 n = len(reads_list) | 54 n = len(reads_list) |
| 55 if n%2 != 0: | 55 if n%2 != 0: |
| 56 exit_and_explain('Problem with pairing reads filename and reads label') | 56 exit_and_explain('Problem with pairing reads filename and reads label') |
| 57 if format == 'bam': | |
| 58 input2_args = '--bam' | |
| 59 elif format == 'begraph': | |
| 60 input2_args = '--bedgraph' | |
| 57 input2_args='-i' | 61 input2_args='-i' |
| 58 k = 0 | 62 k = 0 |
| 59 reads_filenames = [''] * (n/2) | 63 reads_filenames = [''] * (n/2) |
| 60 reads_labels = [''] * (n/2) | 64 reads_labels = [''] * (n/2) |
| 61 for i in range(0, n, 2): | 65 for i in range(0, n, 2): |
| 64 reads_labels[k] = re.sub(r' ', '_', cur_label) | 68 reads_labels[k] = re.sub(r' ', '_', cur_label) |
| 65 if not reads_labels[k]: | 69 if not reads_labels[k]: |
| 66 reads_labels[k] = 'sample_%s' % str(k) | 70 reads_labels[k] = 'sample_%s' % str(k) |
| 67 input2_args='%s "%s" "%s"' % (input2_args, reads_filenames[k], reads_labels[k]) | 71 input2_args='%s "%s" "%s"' % (input2_args, reads_filenames[k], reads_labels[k]) |
| 68 k += 1 | 72 k += 1 |
| 69 if format == 'bedgraph': | |
| 70 input2_args = input2_args + ' --bedgraph' | |
| 71 return input2_args, reads_filenames, reads_labels | 73 return input2_args, reads_filenames, reads_labels |
| 72 | 74 |
| 73 def redirect_errors(alfa_out, alfa_err): | 75 def redirect_errors(alfa_out, alfa_err): |
| 74 # When the option --n is enabled, alfa prints '### End of the program' in stderr even if the process worked- | 76 # When the option --n is enabled, alfa prints '### End of the program' in stderr even if the process worked- |
| 75 # The following lines to avoid the tool from crashing in this case | 77 # The following lines to avoid the tool from crashing in this case |