Alexey Morozov | 26 Sep 04:32 2013
Picon

Re: Fetching particular tags of genbank/genpept features via eutils

Yes, I already did something like that - downloaded feature tables from
NCBI site. Sorry again for asking questions unrelated to bioperl.

2013/9/26 Jason Stajich <jason.stajich <at> gmail.com>

> More likely you want another place to ask the question - biostars perhaps
> - http://www.biostars.org/
>
> if you were only searching genomes you could perhaps grab the ptt files
> from the FTP site - though you would need to lookup GI ids to get the ACC
> number for the NP_XX which is a bit convoluded and I'm not sure you can
> round trip.
>
> But the produce descriptions for the genomes like in bacteria are in these
> .ptt files.
> ftp.ncbi.nih.gov:
> /genomes/Bacteria/Yersinia_pestis_A1122_uid158119/NC_017169.ptt
>
> Jason
>
> On Sep 24, 2013, at 11:00 PM, Alexey Morozov <alexeymorozov1991 <at> gmail.com>
> wrote:
>
> > Dear colleagues,
> > I'm not sure if this list is the right place to ask, but I have a
> question
> > regarding NCBI eutils. Say, I have lots of CDS's IDs like NP_769305.1 or
> > YP_001638012.1. "Lots" as in "Millions of them" (a metagenomic project).
> Of
> > course, I want to get something actually meaningful, so I decided to use
> > "product" field of associated protein records. Can I spare fetching
> > complete records, which will easily be gygabytes upon gigabytes of
> > unnecessary data and get at least only "protein" feature of genpept file?
> >
> > --
> > Alexey Morozov,
> > LIN SB RAS, bioinformatics group.
> > Irkutsk, Russia.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l <at> lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Jason Stajich
> jason.stajich <at> gmail.com
> jason <at> bioperl.org
>
>

--

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

Gmane