I want to extract specific CDS from a gbk file into another gbk file. Apparently it is not so trivial.
I can read here how to slice a genbank so I do the following:
record = SeqIO.read("SpeciesA.gbk", "genbank") sub_record=(record[25500:33500]) SeqIO.write(sub_record, "test.gbk", "genbank")
This seems to work quite well, but I have problem to read draft genomes were I have multiple contigs.
When I try to import them I get:
record = SeqIO.read("SpeciesB.gbk", "genbank") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.7/dist-packages/Bio/SeqIO/__init__.py", line 656, in read raise ValueError("More than one record found in handle") ValueError: More than one record found in handle
I did not manage to find a way around it, any idea how to fix this?