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Gmane
From: Alexey Morozov <alexeymorozov1991 <at> gmail.com>
Subject: Re: Fetching particular tags of genbank/genpept features via eutils
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 26th September 2013 02:32:35 UTC (over 3 years ago)
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 <[email protected]>

> 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

> 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
> > [email protected]
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Jason Stajich
> [email protected]
> [email protected]
>
>


-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
 
CD: 2ms