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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Tmhmm 3pm"
.TH Bio::Tools::Tmhmm 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Tools::Tmhmm \- parse TMHMM output (TransMembrane HMM)
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&  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;
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\s-1TMHMM\s0 is software for the prediction of transmembrane helices in proteins.
See  <http://www.cbs.dtu.dk/services/TMHMM/> for more details.
.PP
This module parses the \*(L"long output\*(R" format of \s-1TMHMM 2.0\s0 and
creates a Bio:SeqFeature::Generic object for each \f(CW\*(C`TMHelix\*(C'\fR feature found
from lines like this:
.PP
.Vb 1
\&  my_sequence_id  TMHMM2.0  TMhelix     54    76
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Torsten Seemann"
.IX Header "AUTHOR - Torsten Seemann"
Email torsten.seemann \s-1AT\s0 infotech.monash.edu.au
.SH "CONTRIBUTOR \- Bala"
.IX Header "CONTRIBUTOR - Bala"
Email savikalpa@fugu\-sg.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 7
\& 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
.Ve
.SS "next_result"
.IX Subsection "next_result"
.Vb 5
\& Title   : next_result
\& Usage   : my $feat = $Tmhmm\->next_result
\& Function: Get the next result set from parser data
\& Returns : Bio::SeqFeature::Generic
\& Args    : none
.Ve