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[Bugfix] Fix issue where re-running inference pipeline could result in a file-not-found error #3

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Merged
merged 2 commits into from
Oct 27, 2021
Merged

[Bugfix] Fix issue where re-running inference pipeline could result in a file-not-found error #3

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e62b87a
Add logic to construct filepaths for already-postprocessed input pair…
amorehead Oct 27, 2021
edd23fd
Scan directory of postprocessed pairs to determine how to construct i…
amorehead Oct 27, 2021
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20 changes: 17 additions & 3 deletions project/utils/deepinteract_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -721,13 +721,27 @@ def convert_input_pdb_files_to_pair(left_pdb_filepath: str, right_pdb_filepath:
pruned_dataset=os.path.join(input_dataset_dir, 'interim', 'parsed'),
hhsuite_db=hhsuite_db,
output_dir=os.path.join(input_dataset_dir, 'interim', 'external_feats'))
# Only a single pair file is produced in this case
pair_filepath = launch_postprocessing_of_pruned_pairs(
# Postprocess any pruned pairs that have not already been postprocessed
pair_filepaths = launch_postprocessing_of_pruned_pairs(
raw_pdb_dir=os.path.join(input_dataset_dir, 'raw'),
pruned_pairs_dir=os.path.join(input_dataset_dir, 'interim', 'pairs'),
external_feats_dir=os.path.join(input_dataset_dir, 'interim', 'external_feats'),
output_dir=os.path.join(input_dataset_dir, 'final', 'raw')
)[0]
)
if len(pair_filepaths) > 0:
# Retrieve the filepath of the single input pair produced in this case
pair_filepath = pair_filepaths[0]
else:
# Manually construct the already-postprocessed input pair's filepath since no pairs needed postprocessing
pruned_pairs_dir = os.path.join(input_dataset_dir, 'interim', 'pairs')
output_dir = os.path.join(input_dataset_dir, 'final', 'raw')
produced_filenames = db.get_structures_filenames(output_dir, extension='.dill')
produced_keys = [db.get_pdb_name(x) for x in produced_filenames if db.get_pdb_name(x) in left_pdb_filepath]
pdb_filename = [os.path.join(pruned_pairs_dir, db.get_pdb_code(key)[1:3], key)
for key in produced_keys][0]
sub_dir = output_dir + '/' + db.get_pdb_code(pdb_filename)[1:3]
pair_filepath = sub_dir + '/' + db.get_pdb_name(pdb_filename)
# Impute any missing feature values in the postprocessed input pairs
impute_missing_feature_values(output_dir=os.path.join(input_dataset_dir, 'final', 'raw'))
# Load preprocessed pair
with open(pair_filepath, 'rb') as f:
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