Python Programming for Biology: Bioinformatics and Beyond

Accessing public databases

If, rather  than  getting a  sequence  record from  a  file,  we wish  to  get data  directly  from  a

database then there are a few helper functions in BioPython that allow easy access to some

large  sequence  databases  via  Internet-based  services,  rather  than  having  to  talk  to  the

database  directly.  For  example,  if  we  wish  to  read  a  FASTA-format  file  from  NCBI

GenBank we can do the following, although we naturally have to know the identifier for

the sequence we want.

We import the Entrez module, set the email address attribute (to identify ourselves, as

encouraged  by  the  database)  and  then  call  a  function  to  fetch  a  given  entry  based  on  a

given database type “protein”, return format type “fasta” and sequence identifier number.

from Bio import Entrez

Entrez.email = '[e-mail]'

socketObj = Entrez.efetch(db="protein", rettype="fasta",

id="71066805")

---

The  above  function  call  gives  back  an  open  socket  object  (assuming  the  connection

works) that can be used in the same way as a normal open file object, although it actually

represents a connection via the Internet. Hence, the reading of the sequence is done in the

same way as for the FASTA file:

dnaObj = SeqIO.read(socketObj, "fasta")

socketObj.close()

print(dnaObj.description)

print(dnaObj.seq)

In  a  similar  way  we  can  read  a  SWISSPROT  record  using  the  ExPASy  module,

although it should be noted that the function to find the sequence and get an open socket

(get_sprot_raw)  is  different  to  before  and  requires  different  arguments,  given  that  such

specifications  depend  on  the  exact  details  of  the  Internet  service  that  the  database

provides.

from Bio import ExPASy

socketObj = ExPASy.get_sprot_raw('HBB_HUMAN')

proteinObj = SeqIO.read(socketObj, "swiss")

socketObj.close()

print(proteinObj.description)

print(proteinObj.seq)