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// PSI-Blast commandline version using Biopython
// July 20, 2011 at 11:10 AM

http://biostar.stackexchange.com/questions/10442/psi-blast-commandline-version-using-biopython
Hi Niek,

I have been trying to get my program for PSI-Blast run, i have been using the wrapper from Bio.Blast.Applications.NcbipsiblastCommanline:
I saw the code you posted at http://biostar.stackexchange.com/questions/2515/how-to-parse-psiblast-results-using-biopython-and-blast-2-2-24

i tried to use the same but it doesnt seem to work for me. can you suggest me why?

code that i used:

    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)
    str(psi_cline)
    psi_cline()


here is the error that i get :
Traceback (most recent call last):
  File "psiBlast.py", line 116, in 
    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 do not get any XML as my output as the command is not found apparently.
in this case queryID is a protein name and the queryID.fasta consists of the fasta file.

looking forward for your reply.
Molly


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