| Bio::Tools::Tmhmm(3pm) | User Contributed Perl Documentation | Bio::Tools::Tmhmm(3pm) |
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:
my_sequence_id TMHMM2.0 TMhelix 54 76
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Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
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Email torsten.seemann AT infotech.monash.edu.au
Email savikalpa@fugu-sg.org
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
| 2021-08-15 | perl v5.32.1 |