[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.


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
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben

More information about the Bioperl-l mailing list