[Biopython] PSI-BLAST

[molly mutant]

Can anyone please share the functioning codes for PSI-BLAST using NCBI
commandline or suggest me the source from where i can get it?? i am in an
urgent need of it :( and i can not find the problem with my command/code.

Regards,
Molly

On Wed, Jul 20, 2011 at 4:19 PM, molly mutant <mollymutant at googlemail.com>wrote:

> if it use cline() command:
>
>         psi_cline = NcbipsiblastCommandline('psiblast', db =
> 'refseq_protein',\
>                                             query = queryID+".fasta",
> evalue =  10 , \
>                                             out = queryID+"_psi.xml",
> outfmt = 7, \
>                                             out_pssm = queryID+"_pssm")
>         str(psi_cline)
>         psi_cline()
>
> the following error occurs :
> Traceback (most recent call last):
>   File "psiBlast.py", line 113, in <module>
>     psi_cline()
>   File
> "/usr/local/lib/python2.6/dist-packages/biopython-1.57-py2.6-linux-x86_64.egg/Bio/Application/__init__.py",
> line 432, in __call__
>     stdout_str, stderr_str)
> Bio.Application.ApplicationError: Command 'psiblast -out NP_012649_psi.xml
> -outfmt 7 -query NP_012649.fasta -db refseq_protein -evalue 10 -out_pssm
> NP_012649_pssm' returned non-zero exit status 127, '/bin/sh: psiblast: not
> found'
>
> I think this error stands for that the command is not found, which means
> that my command is incorrect, am i right??
>
>
>
> On Wed, Jul 20, 2011 at 3:33 PM, molly mutant <mollymutant at googlemail.com>wrote:
>
>> 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
>>>>>
>>>>