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>.
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