Psi-Blast Commandline Version Using Biopython

Question

[Molly]

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 <module> psicline() File "/usr/local/lib/python2.6/dist-packages/biopython-1.57-py2.6-linux-x8664.egg/Bio/Application/init.py", line 432, in call stdoutstr, stderrstr) Bio.Application.ApplicationError: Command 'psiblast -out NP012649psi.xml -outfmt 7 -query NP012649.fasta -db refseqprotein -evalue 10 -outpssm NP012649_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

[Michael Schubert]

Hi Molly! Please don't cross-post on the BioPython Mailing List and here. Reference: http://lists.open-bio.org/pipermail/biopython/2011-July/007450.html

Answer 1

[Peter]

As Michael pointed out, you've already been discussing this on the Biopython mailing list where people have tried to explained the error message probably means you have not installed the BLAST+ command line tools (in this case the binary psiblast), or the binaries are not on the Unix PATH (in which case update the PATH environment variable, or use the explicit full path to the binary). http://lists.open-bio.org/pipermail/biopython/2011-July/007453.html

Answer 2

[Molly]

Sorry people for the cross question. but i posted it here when nobody was replying me :( anyways, my problem is solved now.

Thanks for the help.