Ad hoc fixes to make nerpa 1.1 run on mibig inputs #22
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azmtag
commented
Mar 10, 2024
| @@ -78,6 +78,8 @@ def __init__(self, domain_prediction): | |||
| self.small_cluster_pred = prediction_data['small_cluster_pred'] | |||
| self.single_amino_pred = prediction_data['single_amino_pred'] | |||
| self.uncertain = prediction_data['uncertain'] | |||
| else: | |||
| raise RuntimeError('Neither "nrpys" nor "NRPSPredictor2" in domain prediction.') | |||
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BGC0001329 and BGC0002100 cause this exception
… Skip BGCs exceeding this limit.
azmtag
commented
Mar 10, 2024
| 0, predictions_info_list, dirname) | ||
| except KeyboardInterrupt as e: | ||
| raise e | ||
| except Exception as e: |
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BGC0002095 causes
Traceback (most recent call last):
File "/home/azat/tools/nerpa-1-1/bin/nerpa.py", line 355, in <module>
run(args, log)
File "/home/azat/tools/nerpa-1-1/bin/nerpa.py", line 305, in run
path_predictions = predictions_preprocessor.create_predictions_by_antiSMASH_out(get_antismash_v3_compatible_input_paths(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/azat/tools/nerpa-1-1/share/nerpa/nerpa_pipeline/predictions_preprocessor.py", line 89, in create_predictions_by_antiSMASH_out
handle_helper.debug_print_parts(dirname, parts, orf_domains, orf_ori, orf_pos)
File "/home/azat/tools/nerpa-1-1/share/nerpa/nerpa_pipeline/handle_helper.py", line 139, in debug_print_parts
print(cur_orf + "[" + str(orf_pos[cur_orf][0]) + "-" +
~~~~~~~^^^^^^^^^
KeyError: 'ctg1_extra_gene'
azmtag
commented
Mar 10, 2024
| handle_helper.debug_print_parts(dirname, parts, orf_domains, orf_ori, orf_pos) | ||
|
|
||
| if len(parts) > 100: | ||
| raise RuntimeError(f'Too many parts: {len(parts)}') |
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BGC0000459: 347 parts
BGC0001033: 34460 parts
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This is a technical PR to keep track of my ad-hoc changes