[Bioperl-l] UNIPROT foo.tsv files support

[Dave Howorth]

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
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
>