[Biopython] PSI-BLAST

[João Rodrigues]

Dear Molly,

I never worked with that module so this might be wrong. But from my
experience, that error is common when you have aliased the executable, which
doesn't work. Try adding the directory where the executable 'psiblast' is
(usually something /bin) to your PATH variable:

export PATH="${PATH}:/my/blast/directory/bin/'

Troubleshooting and debugging are parts of coding, so I'd recommend you to
spend half an hour on this and I'm sure you'll get i through.

Best,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



On Wed, Jul 20, 2011 at 5:30 PM, molly mutant <mollymutant at googlemail.com>wrote:

> 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
> >>>>>
> >>>>
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