[Bioperl-l] UNIPROT foo.tsv files support

[Brian Osborne]

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