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How To Get A Blast Record From Stdout Of Ncbiblastxcommandline

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i am blasting sequences from a fasta file individually since the output will be handled differently depending on the quality of the hit.

currently i have this, which works fine:

blast_handle = Blastx_Command(stdin=seq_record.format("fasta"))

however, this involves writing the output to a temporary xml file and then reading it with NCBIXML.parse(file), which is quite slow.

NCBIXML.read() or parse() expects a file, so as far as i understand, it cannot directly take the standard output.

does anyone know a way to take the stdout from the Blastx_Command and somehow turn that into a BlastRecord?

thanks in advance


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