0.2.2 fixed tsv bug in predict

.gitignore

@@ -127,3 +127,5 @@ dmypy.json
 /esm2_embs_3B
 *.sh
 draft.py
+/data/string_species/mmseqs_dbs/
+/data/human_virus/all_test_viruses.csv

senseppi/__init__.py

-__version__ = "0.2.1"
+__version__ = "0.2.2"
 __author__ = "Konstantin Volzhenin"
 
 from . import model, commands, esm2_model, dataset, utils, network_utils

senseppi/commands/predict.py

@@ -99,13 +99,20 @@ def main(params):
     logging.info('Predicting...')
     preds = predict(params)
 
-    data = pd.read_csv(params.pairs_file, delimiter='\t', names=["seq1", "seq2"])
+    data = pd.read_csv(params.pairs_file, delimiter='\t')
+    #if 3 columns, then assign names ['seq1', 'seq2', 'label'] if 2 columns, then names ['seq1', 'seq2']
+    if len(data.columns) == 3:
+        data.columns = ['seq1', 'seq2', 'label']
+    elif len(data.columns) == 2:
+        data.columns = ['seq1', 'seq2']
+    else:
+        raise ValueError('The pairs file must have 2 or 3 columns: seq1, seq2 and label(optional)')
     data['preds'] = preds
 
-    data.to_csv(params.output + '.tsv', sep='\t', index=False, header=False)
+    data.to_csv(params.output + '.tsv', sep='\t', index=False, header=True)
 
     data_positive = data[data['preds'] >= params.pred_threshold]
-    data_positive.to_csv(params.output + '_positive_interactions.tsv', sep='\t', index=False, header=False)
+    data_positive.to_csv(params.output + '_positive_interactions.tsv', sep='\t', index=False, header=True)
 
 
 if __name__ == '__main__':