add signal peptides to output #32

oschwengers · Jan 18, 2022 · 4f8e23b · 4f8e23b
1 parent 8f18f36
commit 4f8e23b
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/bakta/main.py b/bakta/main.py
@@ -487,6 +487,7 @@ def main():
     cdss = [f for f in features if f['type'] == bc.FEATURE_CDS]
     print(f"\tCDSs: {len(cdss)}")
     print(f"\t  hypotheticals: {len([cds for cds in cdss if 'hypothetical' in cds])}")
+    print(f"\t  signal peptides: {len([cds for cds in cdss if bc.FEATURE_SIGNAL_PEPTIDE in cds])}")
     print(f"\tsORFs: {len([f for f in features if f['type'] == bc.FEATURE_SORF])}")
     print(f"\tgaps: {len([f for f in features if f['type'] == bc.FEATURE_GAP])}")
     print(f"\toriCs/oriVs: {len([f for f in features if (f['type'] == bc.FEATURE_ORIC or f['type'] == bc.FEATURE_ORIV)])}")
@@ -565,6 +566,7 @@ def main():
         fh_out.write(f"CRISPR arrays: {len([f for f in features if f['type'] == bc.FEATURE_CRISPR])}\n")
         fh_out.write(f"CDSs: {len(cdss)}\n")
         fh_out.write(f"hypotheticals: {len([cds for cds in cdss if 'hypothetical' in cds])}\n")
+        fh_out.write(f"signal peptides: {len([cds for cds in cdss if bc.FEATURE_SIGNAL_PEPTIDE in cds])}\n")
         fh_out.write(f"sORFs: {len([f for f in features if f['type'] == bc.FEATURE_SORF])}\n")
         fh_out.write(f"gaps: {len([f for f in features if f['type'] == bc.FEATURE_GAP])}\n")
         fh_out.write(f"oriCs: {len([f for f in features if f['type'] == bc.FEATURE_ORIC])}\n")