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Biopython NcbiblastpCommandline not working: "No such file or directory: 'test.xml"
from Bio.Blast.Applications import NcbiblastpCommandline
blastp=r"C:\NCBI\blast-BLAST_VERSION+\bin\blastp.exe"
blastp_cline = NcbiblastpCommandline(blastp, query=r"C:/NCBI/blast-BLAST_VERSION+/bin/test.fasta", db=r'C:/NCBI/blast-BLAST_VERSION+/bin/bos_protein.fasta', outfmt=5, evalue=0.00001, out=r"C:/NCBI/blast-BLAST_VERSION+/bin/test.XML")
blastp_cline


from Bio.Blast import NCBIXML
with open("test.XML") as result_handle:
    E_VALUE_THRESH=0.01
    blast_records = NCBIXML.parse(result_handle)
    blast_record = NCBIXML.read(result_handle)
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            if hsp.expect < E_VALUE_THRESH:
                print("****Alignment****")
                print("sequence:", alignment.title)
                print("length:", alignment.length)
                print("e value:", hsp.expect)
                print(hsp.query[0:75] + "...")
                print(hsp.match[0:75] + "...")
                print(hsp.sbjct[0:75] + "...")

Trying to do a local blast using NCBIBLAST+, already downloaded in the mentioned path. I am using Win10 and Spyder. I have my database created as well as the fasta files contain only protein sequences. Still .XML file is not getting created and also the blastp_cline variable is not getting created. Thanks in advance

biopython
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updated by Mensur Dlakic Mensur Dlakic • written by saubhiksom • saubhiksom

How about you tell us the exact error with line numbers?

With the information we have, it seems like you are saving the file in C:/NCBI/blast-BLAST_VERSION+/bin/test.XML, but then you are parsing test.XML. Why not parse from the same file where you saved the results?

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written by Mensur Dlakic Mensur Dlakic

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