doubt loading pages

[Peter Otten]

José Manuel Suárez Sierra wrote:

> hello everyone,
> Im trying to make a program that takes an archive from pdb (for instance
> this link http://www.rcsb.org/pdb/files/fasta.txt?structureIdList=5HXY
> 
> after reading it I want it to save in a list only this part of the
> archive:
> 
> MGSSHHHHHHSSGLVPRGSHMASMTGGQQ...IRFIQQILGHASVATTQIYTHLNDSALREMYTQHRPRY
> 
> I have written this:
> 
> import urllib2
> 
> 
> seq=raw_input("Introduce pdb code \n")
> 
> 
> 
> seq =
> urllib2.urlopen(
> "http://www.rcsb.org/pdb/files/fasta.txt?structureIdList="+seq)
> print seq.read()
> 
> 
> seq.close()
> 
> 
> My question is, how do I save this into a python list?

While you could cook up something yourself it's probably better to use an 
existing library like biopython.

$ cat retrieve_fasta.py
import urllib2
import Bio.SeqIO

seq = raw_input("Introduce pdb code \n")

seq = urllib2.urlopen(
    "http://www.rcsb.org/pdb/files/fasta.txt?structureIdList="
    + seq
)

for record in Bio.SeqIO.parse(seq, "fasta"):
    seq_list = list(record.seq.tostring())
    break # stop after the first iteration

print seq_list
$ python retrieve_fasta.py
Introduce pdb code 
5HXY
['M', 'G', 'S', 'S', 'H', 'H', 'H', 'H', 'H', 'H', 'S', 'S', 'G', 'L', 'V',
...
'R', 'Y']

See <http://biopython.org/wiki/SeqIO>.