I need to remove features from a gbk file that have split coordinates:
join{[5355286:5355459](+), [0:17](+)}
join{[5355286:5355459](+), [0:17](+)}
So far i was able to test features to check if they are CompaundLocation types, but i culd not remove all off then from the record object:
#!/usr/bin/env python
from Bio import SeqIO
import sys
records = SeqIO.parse(sys.argv[1],"genbank")
for record in records:
for index, feature in enumerate(record.features):
try:
if feature.location.operator == "join":
record.features.pop(index)
except:
pass
SeqIO.write(record, "out.gbk", "genbank")