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