Trimming local GB file with Biopython

Question

[13dsc]

I was wondering if I could use Biopython in order to trim a local gb file.

Ex. I have a 100kb gb file but I am interested in a continuous 25kb portion. I know the location of the start and stop of the 25kb region. How do I create a gb file which contains only that 25kb portion from the larger file.

[st.ph.n]

You can. Look into into SeqIO, and string slicing.

[13dsc]

will that keep the gene annotations associated with the gb file for that slice?

[st.ph.n]

Yes, just edit the seq record, and output the Seq object to a new file.

Answer 1

[Joe]

I wrote a script that does exactly this a while back.

https://github.com/jrjhealey/bioinfo-tools/blob/master/Genbank_slicer.py