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Bio.Blast and Blast version compatability

I am trying to use Bio.Blast for parsing my blast output..but biopoython-1.65 says the Bio.Blast is going to be deprecated and replaced by Bio.SearchIO.

since I have Blast output in Plain-text format..I am trying to use BlastParser and PsiblastParser included in Bio.Blast.NCBIStandalone module.

I have few doubts regarding this..

  1. I like to know the Bio.SearchIO, Bio.Blast is compatible with what version's of Blast? And can we use Bio.SearchIO for parsing plain-text format outputs in future?
  2. I couldn't find PsiBlastParser in plain-text output format parser in Bio.SearchIO.If available please do mention.
biopython blast bio.blast
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updated by Ram Ram • written by nvijay.1991 • nvijay.1991

1 answer

Currently Bio.SearchIO uses Bio.Blast.NCBIStandalone internally to parse the plain text BLAST output, but as you have noticed from the warnings the plain text parser is deprecated. We (and the NCBI) do not recommend parsing this. You should consider the tabular, CSV, XML, or JSON, etc output formats instead.

The same applies to PsiBlastParser again for plain text output, but that was never exposed via SearchIO.

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written by Peter Peter

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