[Biopython] PSI-BLAST

[molly mutant]

Oh, i forgot to mention :

queryID here is a protein ID for example NP_010247.1
 ' query = queryID+".fasta" ' is a fasta file for this protein.
i want to get the XML output from the psi blast.

Regards
Molly

On Wed, Jul 20, 2011 at 3:26 PM, molly mutant <mollymutant at googlemail.com>wrote:

> hello all,
>
> I was also trying to run my program using the same wrapper from
> Bio.Blast.Application for psiblast commandline.
>
> i use the following code but this is not generating XML file.
>         psi_cline = NcbipsiblastCommandline('psiblast', db =
> 'refseq_protein', query = queryID+".fasta", evalue =  10 , out =
> queryID+"_psi.xml", outfmt = 7, out_pssm = queryID+"_pssm")
>         p =
> subprocess.Popen(str(psi_cline),stdout=subprocess.PIPE,stderr=subprocess.PIPE,shell=(sys.platform!="win32"))
>         blastParser(p.stdout)
>
> i have defined blastParser for parsing XML files which works perfectly with
> other xml files.
>
> i get the following error :
>
> Traceback (most recent call last):
>   File "psiBlast.py", line 110, in <module>
>     blastParser(p.stdout)
>
>   File
> "/usr/local/lib/python2.6/dist-packages/biopython-1.57-py2.6-linux-x86_64.egg/Bio/Blast/NCBIXML.py",
> line 617, in parse
>     raise ValueError("Your XML file was empty")
> ValueError: Your XML file was empty
>
>
> you can see that i am using python 2.6 and Biopython 1.57. Do you know
> where am i going incorrect?
>
> Molly
>
> On Wed, Jul 20, 2011 at 3:07 PM, malvika sharan <malvikasharan at gmail.com>wrote:
>
>
>>
>> ---------- Forwarded message ----------
>>
>>
>> Thank you Peter and Eric.
>>
>> you are right and i think i should have known this :(
>> I updated Biopython. and revising my codes. it should work now.
>>
>> Malvika
>>
>>
>> On Tue, Jul 19, 2011 at 8:08 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
>>
>>> On Monday, July 18, 2011, Eric Talevich <eric.talevich at gmail.com> wrote:
>>> > On Sun, Jul 17, 2011 at 7:27 PM, malvika sharan <
>>> malvikasharan at gmail.com>wrote:
>>> >
>>> >> My OS is mac, Python is 2.7 as mentioned,Biopython 1.50.
>>> >>
>>> >
>>> > That's a very old version of Biopython. Are you able to install a more
>>> > recent version?
>>> >
>>> >
>>> > And well as i said that the the error shows at the import.
>>> >> import os, sys
>>> >> from Bio import SeqIO
>>> >> from Bio import Entrez
>>> >> from Bio.Blast import NCBIWWW*
>>> >> *from Bio.Blast.NCBIStandalone import PSIBlastParser
>>> >> *from Bio.Blast.Applications import NcbipsiblastCommandline*
>>> >> from Bio.Blast import NCBIXML
>>> >>
>>> >
>>> > If the earlier imports of SeqIO and Entrez work, then
>>> > NcbipsiblastCommandline probably wasn't included in Biopython 1.50, I
>>> would
>>> > guess.
>>> >
>>>
>>> Correct. The BLAST+ wrappers were added in Biopython 1.53.
>>> You will need to update it, ideally to the current release, 1.57
>>>
>>> In general if some imports work and others fail, your library
>>> Is either too old (and what you want didn't exist in the old
>>> version), or too new (the code you want to use was obsolete
>>> and removed).
>>>
>>> Peter
>>>
>>
>>
>>
>