How To Retrive Selected Region From Each Protein In A Multiple Fasta File

Question

[friveroll]

With this list from blast results, first column for name, second start position and third end position.

gi|6226847|sp|Q13324.2|CRFR2_HUMAN 366 411
gi|1345735|sp|P47866.1|CRFR2_RAT 366 411
gi|2495061|sp|Q60748.1|CRFR2_MOUSE 386 431
gi|3023564|sp|O42603.1|CRFR2_XENLA 368 413
gi|3023563|sp|O42602.1|CRFR1_XENLA 370 415
gi|2495062|sp|Q90812.1|CRFR1_CHICK 375 420
gi|3913367|sp|O62772.1|CRFR1_SHEEP 370 415
gi|75053365|sp|Q76LL8.1|CRFR1_MACMU 370 415
gi|544100|sp|P35347.1|CRFR1_MOUSE 370 415
gi|461836|sp|P34998.1|CRFR1_HUMAN 399 444
gi|544101|sp|P35353.1|CRFR1_RAT 370 415

Edit: Finally I've got it here is the code inspired in this post

from Bio import Entrez
from Bio import SeqIO

Entrez.email = '[e-mail]'
filename = 'out_region.fasta'

with open('list2.txt', 'r') as fd:
    for line in fd:
      gi=line.split('|')[1]
      start=line.split(' ')[1]
      end =line.split(' ')[2].rstrip("\n")
      handle = Entrez.efetch(db='protein',
      rettype='fasta', 
      retmode='text', 
      seq_start=int(start), 
      seq_stop=int(end), 
      id = gi)

      rec = SeqIO.read(handle, 'fasta')

      out_handle = open(filename,'a')
      SeqIO.write(rec, out_handle, 'fasta')
      out_handle.close()
      handle.close()

[friveroll]

I modify the code, but I can only write the first record to a fasta file

Answer 1

[raunakms]

Here is my answer to a similar post but this one uses BioPerl

http://www.biostars.org/post/show/13659/how-can-i-programmatically-retrieve-the-genbank-records-with-accession-numbers-in-the-form-jn/#18429

There must be a similar GenBank parser in BioPython just dig into its website !!