[Bioperl-l] UNIPROT foo.tsv files support

[Alexey Morozov]

Truly they are! Sorry for messing up databases.


2013/4/10 Dave Howorth <dhoworth at mrc-lmb.cam.ac.uk>

> Alexey Morozov wrote:
> > 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.
>
> They are InterPro rather than UniProt!
>
> > 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.
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
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> >>
> >
> >
>
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-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.