Rearranging a Genbank file

[sjlabrie]

Hi all,

I would like to set the origin of a sequence at a different site. For example, phiX174 the origin is set in the gene A, and to generate figure, I would like to move it upstream the gene to avoid the complication of the join(3981..5386,1..136) annotation du to the circular genome. Usually, I am using the very simple script bellow to move the origin:

from Bio import SeqIO
import sys
origin = int(sys.argv[2])
rec = SeqIO.read(sys.argv[1],'genbank')
rec_rea = rec[origin:]+rec[:origin]
SeqIO.write(rec_rea,sys.argv[1][:-3]+'_rea.gb','genbank')

But I am loosing the Gene A this way... Any suggestion ?

Simon

[maubp]

As the Biopython tutorial tried to explain, you are losing this gene when slicing the SeqRecord, and will have to manually have to deal with it (add a new SeqFeature).

A more general 'roll' method might be added to a future Biopython release which could take care of this (rolling a circular genome - unless you can think of a better method name?).