Retrieving batch of selected regions sequences from a NCBI db

Question

[emilia.skirmuntt]

Hi,

I was wondering if there is any way of downloading a batch of selected regions from sequences from Genbank. I have several accession numbers for different contigs but I need only selected regions from them and not full sequences. Is there any way to download them in a batch and not doing that one by one, because that will take me ages to finish?

[emilia.skirmuntt]

Ok, it seems that with Efetch I can still download one sequence fragment at a time (or I'm just missing something, but I was trying for a while now with different options and still no success. I need to download 180 fragments of different contigs and it is getting a bit silly. I was thinking about using Biopython and their Entrez and SeqIO but I got kind of stuck. Input is a file which looks more or less like that:

NW_005871339.1  1   18951   28640
NW_005872753.1  1   4797    13835
NW_005872103.1  1   20997   29747
NW_005878789.1  1   0   5645

What I have so far. But not sure if that even has any chances to work in that form ...

from Bio import Entrez
from Bio import SeqIO

Entrez.email = "mail'
db = "nuccore"

input = SeqIO.parse('input.fasta', 'r')
output = open('output.fasta', 'w')

handle = Entrez.efetch(db=db, id=input[0], strand=input[1], seq_start=input[2], seq_end=input[3], rettype="fasta", retmode="text")

[GenoMax]

See if these help: Speed Of Efetch In Biopython
How To Retrieve Multiple Sequence In One Python Script
How To Retrive Selected Region From Each Protein In A Multiple Fasta File

[emilia.skirmuntt]

Great! Thanks for all your help. It seems I need to improve also my search strategy ;)

Answer 1

[GenoMax]

Take a look at Entrez programming utilities from NCBI. Example from the link:

Fetch the first 100 bases of the plus strand of GI 21614549 in FASTA format:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=21614549&strand=1&seq_start=1&seq_stop=100&rettype=fasta&retmode=text

[emilia.skirmuntt]

looks exactly like a thing I'm looking for. Thank you! :)

[GenoMax]

If you have access to NCBI's pre-formatted blast databases you can probably use blastdbcmd to do the same locally with the -range and -entry options.