I am trying to run Blast over protein sequences from two organisms. I downloaded the fasta from NCBI. I am trying to iterate over the list of sequences in the fasta file and do a sequence alignment of each sequence in one file with each sequence in the other. I want to run over local Blast but getting some error, I would greatly appreciate some suggestions.
'''from Bio.Blast.Applications import NcbiblastxCommandline help(NcbiblastxCommandline)''' from Bio.Blast.Applications import NcbiblastpCommandline from StringIO import StringIO from Bio.Blast import NCBIXML from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio import SeqIO from Bio.Blast import NCBIWWW import cStringIO def BlastSeq(): SC_Fasta = open("sc.fsa","r") HS_Fasta = open("hsap.fsa","r") blastp = "C:\\Program Files\\NCBI\\blast-2.2.29+\\bin\\blastp" record1 = list(SeqIO.parse(SC_Fasta,"fasta")) for r1 in record1: r1.id r1.seq record2 = list(SeqIO.parse(HS_Fasta,"fasta")) for r2 in record2: r2.id r2.seq for r1 in record1: for r2 in record2: output = NcbiblastpCommandline(blastp,query= r1.seq, subject=r2.seq, outfmt=5)() blast_result_record = NCBIXML.read(StringIO(output)) def main(): BlastSeq() main() Error: Bio.Application.ApplicationError: Command 'C:\Program Files\NCBI\blast-2.2.29+\bin\blastp -outfmt 5 -query MVKLTSIAAGVAAIAATASATTTLAQSDERVNLVELGVYVSDIRAHLAQYYMFQAAHPTETYPVEVAEAVFNYGDF -subjectHGLQELKAELDAAVLKATGRQILTLRVRLAGAQLSWLYKEATVQEVDVIPEDGAADVRVIISNSAYGKFRKLFPG' returned non-zero exit status -1073741515
I understand that each seq should be passed as individual fasta file,but I don't understand how to proceed.