Question: Trimming local GB file with Biopython
0
gravatar for 13dsc
2.1 years ago by
13dsc0
13dsc0 wrote:

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.

ADD COMMENTlink modified 2.1 years ago by Joe14k • written 2.1 years ago by 13dsc0
1

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

ADD REPLYlink written 2.1 years ago by st.ph.n2.5k

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

ADD REPLYlink written 2.1 years ago by 13dsc0

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

ADD REPLYlink written 2.1 years ago by st.ph.n2.5k
2
gravatar for Joe
2.1 years ago by
Joe14k
United Kingdom
Joe14k wrote:

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

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

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Joe14k
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