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Bio::Blast known bug... any timeline? #132

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markwilkinson opened this issue Nov 7, 2019 · 1 comment
Open

Bio::Blast known bug... any timeline? #132

markwilkinson opened this issue Nov 7, 2019 · 1 comment

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@markwilkinson
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Documentation for Bio::Blast says: "Bug note: When multi-FASTA is given and the format is 7 (XML) or 8 (tab), it should return an array of Bio::Blast::Report objects, but it returns a single Bio::Blast::Report object. This is a known bug and should be fixed in the future."

I can confirm that this is still true.

Is there any timeline for this to be resolved? If someone knows the problem, and can point me in the right direction (save me time looking) I could try to fix it myself...

@ngoto
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ngoto commented Nov 7, 2019

About XML, bio-blastxmlparser, an alternative BLAST XML parser library, may support multi-FAST input.
https://rubygems.org/gems/bio-blastxmlparser

BioRuby native BLAST pasrser was focused on the legacy BLAST. To support current BLAST (BLAST+), I'd like to rewrite it in some days, but not scheduled now...

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