fixes error when amino acids are presented as lower case

pdxgx · Aug 31, 2021 · eb5785f · eb5785f
1 parent 6286d7e
commit eb5785f
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/pepsickle/__init__.py b/pepsickle/__init__.py
@@ -113,23 +113,23 @@ def main():
     elif options.sequence:
         if options.model_type == 'epitope':
             out = predict_protein_cleavage_locations(protein_id="None",
-                                                     protein_seq=options.sequence,
+                                                     protein_seq=options.sequence.upper(),
                                                      model=cleavage_model,
                                                      mod_type="epitope",
                                                      proteasome_type=options.proteasome_type,
                                                      threshold=options.threshold)
 
         elif options.model_type == 'in-vitro-2':
             out = predict_protein_cleavage_locations(protein_id="None",
-                                                     protein_seq=options.sequence,
+                                                     protein_seq=options.sequence.upper(),
                                                      model=cleavage_model,
                                                      mod_type="in-vitro-2",
                                                      proteasome_type=options.proteasome_type,
                                                      threshold=options.threshold)
 
         elif options.model_type == 'in-vitro':
             out = predict_protein_cleavage_locations(protein_id="None",
-                                                     protein_seq=options.sequence,
+                                                     protein_seq=options.sequence.upper(),
                                                      model=cleavage_model,
                                                      mod_type="in-vitro",
                                                      proteasome_type=options.proteasome_type,

diff --git a/pepsickle/model_functions.py b/pepsickle/model_functions.py
@@ -411,7 +411,7 @@ def process_fasta(fasta_file, cleavage_model, verbose=False,  **kwargs):
         if i % 100 == 0 and verbose:
             print("completed:", i, "of", end)
         tmp_out = predict_protein_cleavage_locations(
-            protein_id=protein_id, protein_seq=protein_list[protein_id],
+            protein_id=protein_id, protein_seq=protein_list[protein_id].upper(),
             model=cleavage_model, **kwargs)
 
         for line in format_protein_cleavage_locations(tmp_out):