See answers on https://www.biostars.org/p/140535/
Please don't cross-post the same question to multiple forums (without adding the links), as you waste people's time. There is a lot of overlap between the posters here and on BioStars.
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Question: Is it possible to get local blast output directly in Biopython, without mak
Hi
I am currently filtering through a large amount of reads from a 454 machine. I would like to blast every read against a local blast database and check if the sequence is indeed from a targeted genus/species and not a contaminant. For that I would like to get a direct output to python, so I can read it directly and filter it out if the top matches aren't from the same genus or if the score is too low.
Code:for seq in SeqIO.parse(fasta_file, "fasta"): counter +=1 blast_cline = NcbiblastnCommandline(query="G:\\454 dataset\\new2.fasta", db="database", evalue=0.001, outfmt=5, out="G:\\454 dataset\\blast2.xml") stdout, stderr = blast_cline() print(stdout,stderr) if counter == 1: break
How could I get a stdout output from the local blast? Also is it possible to give the query input a variable and not a file?Tags: None
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