[Bioperl-l] UNIPROT foo.tsv files support

[Alexey Morozov]

These are tab-delimited files which are available for download from
individual pages for families or other groups of proteins, e.g. here
https://www.ebi.ac.uk/interpro/entry/IPR012078/proteins-matched
in top right corner of the page. But I have also decided to make my own
simple parser, especially because I need only a little subset of data
available in files.


2013/4/9 Brian Osborne <bosborne11 at verizon.net>

> Or Bio::SeqIO::table, perhaps.
>
>
> On Apr 9, 2013, at 8:53 AM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
>
> > We support Swissprot format.  You'll have to point out where you
> retrieved the data, TSV isn't listed as a specific file type on their
> downloads page:
> >
> > http://www.uniprot.org/downloads
> >
> > If this is tab-delimited, it should be pretty easy to drum up a custom
> parser using Text::CSV and the Bioperl FASTA parser.
> >
> > chris
> >
> > On Apr 9, 2013, at 2:18 AM, Alexey Morozov <alexeymorozov1991 at gmail.com>
> wrote:
> >
> >> Does BioPerl currently support UNIPROT data? For a couple of families I
> >> have downloaded foo.fasta and foo.tsv files and want to turn data in
> them
> >> to Bio::Seq objects, add taxonomy data and do every kind of fancy stuff
> I
> >> please.
> >> It seems that parsing of UNIPROT tsv files is not described on Bioperl
> wiki
> >> and search for 'uniprot' at CPAN gives only a couple of modules with
> >> totally different functions.
> >> --
> >> Alexey Morozov,
> >> LIN SB RAS, bioinformatics group.
> >> Irkutsk, Russia.
> >> _______________________________________________
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> >
> >
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>


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