remove remnant of terms

oschwengers · Oct 10, 2024 · 51f4d11 · 51f4d11
1 parent ae4142b
commit 51f4d11
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/bakta/features/annotation.py b/bakta/features/annotation.py
@@ -19,6 +19,7 @@
 RE_PROTEIN_NODE = re.compile(r'NODE_', flags=re.IGNORECASE)
 RE_PROTEIN_POTENTIAL_CONTIG_NAME = re.compile(r'(genome|shotgun)', flags=re.IGNORECASE)
 RE_PROTEIN_DOMAIN_CONTAINING = re.compile(r'domain-containing protein', flags=re.IGNORECASE)
+RE_PROTEIN_REMNANT = re.compile(r'Remnant of ', re.IGNORECASE)
 RE_PROTEIN_NO_LETTERS = re.compile(r'[^A-Za-z]')
 RE_PROTEIN_SUSPECT_CHARS_DISCARD = re.compile(r'[.#]')
 RE_PROTEIN_SUSPECT_CHARS_REPLACE = re.compile(r'[@=?%]')
@@ -566,6 +567,11 @@ def revise_cds_product(product: str):
     if(product != old_product):
         log.info('fix product: replace FOG ids. new=%s, old=%s', product, old_product)
 
+    old_product = product
+    product = RE_PROTEIN_REMNANT.sub('', product)  # remove 'Remnant of's
+    if(product != old_product):
+        log.info('fix product: replace remnant ofs. new=%s, old=%s', product, old_product)
+
     old_product = product
     dufs = []  # replace DUF-containing products
     for m in RE_DOMAIN_OF_UNKNOWN_FUCTION.finditer(product):