Python for Bioinformatics: PyCogent 6: NCBI

Saturday, December 5, 2009

PyCogent 6: NCBI

More on PyCogent here. Here are three examples from the cookbook.

• EFetch to obtain a nucleotide sequence from the id
• EUtils to obtain a medline report from Pubmed
• Using a parser to process a Genbank file from disk

import sys
from cogent.db.ncbi import EFetch
from cogent.db.ncbi import EUtils
from cogent.parse.genbank import parse

def test1():
    e = EFetch(db='nucleotide',
               rettype='fasta',
               id='154102')
    result = e.read()
    L = result.split('\n')
    print L[0][:40]
    print L[1][:40]

test1()

>gi|154102|gb|J04243.1|STYHEMAPRF S.typh
GGATCCACTGCCGCAGGCTGTTTAACGGAATCGGCATCCC

def test2():
    e = EUtils(db='pubmed',
               rettype='medline')
    item = e['2544564']  # PMID
    result = item.read()
    print result.split('\n')[0]

test2()

PMID- 2544564

This requires a BioPython file from here.

def test3():
    gb = parse(open('ls_orchid.gbk'))
    print gb.Name
    #print gb.Info
    L = gb.Info['features']
    L = [e for e in L if e['type'] == 'gene']
    print L[0]['gene'][0]

Z78533
5.8S rRNA

Uncomment the line to see all of what is available.