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  • #15

Closed
Open
Opened Oct 01, 2015 by Celine Mercier@mercierOwner

SILVA reference database parsing

Someone would be interested in having obiaddtaxids parse SILVA reference databases (it used to be able to do it but the format probably changed). I'm not sure if there are several SILVA formats or only this one:

>AAAA02038008.4342.6342 Eukaryota;Opisthokonta;Holozoa;Metazoa (Animalia);Eumetazoa;Bilateria;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera;Oryza sativa Indica Group
UCUGGUUGAUCCUGCCAGUAGUU.......
>AAAB01001705.32.640 Eukaryota;Opisthokonta;Holozoa;Metazoa (Animalia);Eumetazoa;Bilateria;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera;Anopheles gambiae str. PEST
UGAUAUACGCUCGUCUCAAAGGU.....

Should I write a parser for that format in obiaddtaxids?

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Reference: obitools/obitools#15