Bio::Tools::Tmhmm - parse TMHMM output (TransMembrane HMM)
use Bio::Tools::Tmhmm; my $parser = Bio::Tools::Tmhmm->new(-fh => $filehandle ); while ( my $tmhmm_feat = $parser->next_result ) { # do something, e.g. push @tmhmm_feat, $tmhmm_feat; }
TMHMM is software for the prediction of transmembrane helices in proteins. See http://www.cbs.dtu.dk/services/TMHMM/ for more details.
This module parses the "long output" format of TMHMM 2.0 and creates a Bio:SeqFeature::Generic object for each TMHelix feature found from lines like this:
TMHelix
my_sequence_id TMHMM2.0 TMhelix 54 76
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::Tools::Tmhmm->new(); Function: Builds a new Bio::Tools::Tmhmm object Returns : Bio::Tools::Tmhmm Args : Either of the following as per L<Bio::Root::IO> interface -fh => $filehandle -file => $filename
Title : next_result Usage : my $feat = $Tmhmm->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.