uhhh no thanks xml is way too verbose. I have over 20M alignments.
Question: Does Biopython parse blast -m8 or -m9 (aka blasttable)? |
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I am getting the following error when I try -m9
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Try with blast's XML output instead. As explained in biopython's FAQs (#17), the XML format is the only one that will be always supported. |
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ParseBlastTable may do what you want, but it was designed for the output of blastpgp, not blastall. I can't get it to work with the BLASTN blasttable I have to hand. |
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Take a look at Biostar question: "How to convert BLAST results to GFF" There is fairly easy Python solution for parsing blast column output. |
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