Changed variable names to work for all sequences. #32

oschwengers · Apr 20, 2021 · 1616876 · 1616876
1 parent 1c45336
commit 1616876
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/bakta/features/signal_peptides.py b/bakta/features/signal_peptides.py
@@ -9,7 +9,7 @@
 
 log = logging.getLogger('SIGNAL_PEPTIDES')
 
-def execute_deepsig(cdss, cds_fasta_path):
+def execute_deepsig(seqs, seqs_fasta_path):
     """Search for Signal Peptides using DeepSig tool."""
     deepsig_output_path = cfg.tmp_path.joinpath('deepsig.gff3')
     if cfg.gram == '?':
@@ -18,7 +18,7 @@ def execute_deepsig(cdss, cds_fasta_path):
         gram = 'gramn' if cfg.gram == '-' else 'gramp'
     cmd = [
         'deepsig.py',
-        '-f', str(cds_fasta_path),
+        '-f', str(seqs_fasta_path),
         '-k', gram,
         '-o', str(deepsig_output_path)
     ]
@@ -34,7 +34,7 @@ def execute_deepsig(cdss, cds_fasta_path):
         log.error('signal peptide: deepsig failed to run through: command=%s, stdout=%s, stderr=%s, error-code=%s', cmd, proc.stdout, proc.stderr, proc.returncode)
         sys.exit('ERROR: deepsig failed to run through! error code: %s, error output: %s', proc.returncode, proc.stderr)
 
-    cds_by_hexdigest = {f"{cds['aa_hexdigest']}": cds for cds in cdss}
+    sequences_by_hexdigest = {f"{seq['aa_hexdigest']}": seq for seq in seqs}
     sig_pep = OrderedDict()
     sig_peps = []
     with deepsig_output_path.open() as fh:
@@ -43,8 +43,8 @@ def execute_deepsig(cdss, cds_fasta_path):
             if feature_type == "Signal peptide":
                 identifier, tool, feature_type, start, stop, feature_annotation_score, placeholder, placeholder2, description = line.split("\t")
                 aa_identifier = identifier.split("-")[0]
-                cds = cds_by_hexdigest[aa_identifier]
-                if cds['strand']=='-':
+                seq = sequences_by_hexdigest[aa_identifier]
+                if seq['strand']=='-':
                     start_nucleotides = start #TODO: figure out correct reverse positions
                     stop_nucleotides = stop
                 else:
@@ -55,8 +55,8 @@ def execute_deepsig(cdss, cds_fasta_path):
                 sig_pep['stop'] = stop_nucleotides
                 sig_pep['feature_annotation_score'] = feature_annotation_score
                 sig_pep['identifier'] = aa_identifier
-                sig_pep['sequence'] = cds['sequence']
-                sig_pep['strand'] = cds['strand']
+                sig_pep['sequence'] = seq['sequence']
+                sig_pep['strand'] = seq['strand']
 
                 sig_peps.append(sig_pep)
     return sig_peps