potential fix for #727, seems to happen if gene removed that has alt-…

…transcript
nextgenusfs · Jun 16, 2022 · 1597d3b · 1597d3b
1 parent a5266cd
commit 1597d3b
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/funannotate/library.py b/funannotate/library.py
@@ -4446,6 +4446,8 @@ def gff2dict(file, fasta, Genes, debug=False, gap_filter=False):
     # loop through and make sure CDS and exons are properly sorted and codon_start is correct, translate to protein space
     for k, v in list(Genes.items()):
         for i in range(0, len(v['ids'])):
+            if not k in Genes:  # capture if gene was removed
+                continue
             if v['type'] in ['mRNA', 'tRNA', 'ncRNA', 'rRNA']:
                 if v['strand'] == '+':
                     sortedExons = sorted(v['mRNA'][i], key=lambda tup: tup[0])