Bio::T...::Tmhmm(3pm)

💖 Bio::Tools::Tmhmm — the vibe check 💖

okay bestie, so this page is the manual for Bio::Tools::Tmhmm (that's the Bio::T...::Tmhmm(3pm) page in the User Contributed Perl Documentation, iykyk). It's a parser. It eats TMHMM output and hands you back features. Let's get into it. 🦋

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✨ NAME ✨

Bio::Tools::Tmhmm — parse TMHMM output (TransMembrane HMM)

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🌸 SYNOPSIS 🌸

literally the whole point, here's how you use it:

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;
}

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🧚 DESCRIPTION 🧚

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

no cap, that's the line it's obsessed with. 💅

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🫶 FEEDBACK 🫶

💌 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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🥺 Support 🥺

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.

🐛 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:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR - Torsten Seemann 👑

Email torsten.seemann AT infotech.monash.edu.au

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🌈 CONTRIBUTOR - Bala 🌈

Email savikalpa@fugu-sg.org

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⭐ APPENDIX ⭐

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

🎀 new 🎀

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

it builds you a whole new object, main character energy fr fr ✨

🎀 next_result 🎀

Title   : next_result
Usage   : my $feat = $Tmhmm->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args    : none

one call, one feature. no args, no drama. 🦋

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💜 okay that's the whole page bestie, you ate it. this was perl v5.32.1, dated 2021-08-15, from the Bio::T...::Tmhmm(3pm) manual — go parse some transmembrane helices, ily 💜