[Bioperl-l] Bio::Tools::TMHMM;

Kai Blin kai.blin at biotech.uni-tuebingen.de
Thu Sep 9 06:16:08 EDT 2010


On Thu, 9 Sep 2010 11:27:23 +0200 (CEST)
"_Lelieveld, Stefan - s1012635" <s1012635 at student.hsleiden.nl> wrote:

Hi Stefan,

> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Tools/Tmhmm.pm : 
> use Bio::Tools::Tmhmm; 
> my $parser = new Bio::Tools::Tmhmm(-fh =>$filehandle ); 
> while( my $tmhmm_feat = $parser->next_result ) { 
> #do something 
> #eg 
> push @tmhmm_feat, $tmhmm_feat; 
> } 
> 
> How do I feed a input.txt(containing the proteins as fasta format) to this parser and how do I save the output? 

You need to run TMHMM first, of course. Bio::Tools::Tmhmm only parses
the TMHMM output file and returns an object that you can ask for
Bio::SeqFeature objects. So if you want to run TMHMM on some fasta
files, this module isn't going to do that for you.

Assuming that input.txt contains the TMHMM output,
"""
my $parser = new Bio::Tools:Tmhmm(-file => "input.txt");
"""
will load parse the TMHMM output for you.

HTH,
Kai

-- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben



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