Question: Is Biopython unable to read draft genomes (having multiple contigs)?
gravatar for dago
4.1 years ago by
dago2.5k wrote:

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 ="SpeciesA.gbk", "genbank")
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 ="SpeciesB.gbk", "genbank")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/dist-packages/Bio/SeqIO/", 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?



ADD COMMENTlink modified 4.1 years ago by geek_y9.4k • written 4.1 years ago by dago2.5k
gravatar for geek_y
4.1 years ago by
geek_y9.4k wrote:

May be you should check this page ?

Use the Bio.SeqIO.parse(handle, format) function if you want to read multiple records from the handle
ADD COMMENTlink written 4.1 years ago by geek_y9.4k

Yes - that's the built-in documentation also available within Python with:

from Bio import SeqIO

Or I would suggest or the main Biopython Tutorial,

ADD REPLYlink written 4.1 years ago by Peter5.8k
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