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

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

✨ NAME ✨

Bio::Tools::Run::Tmhmm — and yeah, the header up top truncates it to Bio::T...:Tmhmm(3pm) because it's a User Contributed Perl Documentation page and the terminal simply ran out of room 💀. Anyway: it's the Object for identifying transmembrane helixes in a given protein seequence. Obsessed. 👑

🦋 SYNOPSIS 🦋

Bestie, here's the whole vibe, copy it exactly like this:

# Build a Tmhmm  factory

# $paramfile is the full path to the seg binary file

my @params = ('PROGRAM',$paramfile);
my $factory = Bio::Tools::Run::Tmhmm->new($param);

# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects

my @feats = $factory->run($seq);

So: build your factory, hand it a Bio::Seq, get your @feats back. Iconic. 🫶

💅 DESCRIPTION 💅

Tmhmm is a program for identifying transmembrane helices in proteins. That's the whole job, and she does it. 💖

⚠️ okay so this part is NOT optional, fr fr: you must have the environmental variable TMHMMDIR set to the base directory where tmhmm and it's associated data/option files reside. And that is NOT the bin directory where the actual executable lives, bestie. The base directory. Not the bin. I said what I said. 🚨

🎀 FEEDBACK 🎀

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. (Translation: they love hearing from you, so say hi 🌸)

📬 Mailing Lists 📬

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

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

(Yes, the original literally has a head2 floating in the middle of that section. We don't gatekeep formatting quirks here. 💀)

👑 AUTHOR - Bala 👑

Email savikalpa@fugu-sg.org — shoutout to Bala, the author, absolute legend. 🫶✨

🌈 APPENDIX 🌈

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

💖 program_name 💖

  • Title: program_name
  • Usage: $factory>program_name()
  • Function: holds the program name
  • Returns: string
  • Args: None

🎀 program_dir 🎀

  • Title: program_dir
  • Usage: $factory->program_dir(@params)
  • Function: returns the program directory, obtained from ENV variable — in this case it is the tmhmm installation directory, not the location of the executable.
  • Returns: string
  • Args: (nothing listed)

🦋 program_path 🦋

  • Title: program_path
  • Usage: my $path = $factory->program_path();
  • Function: Builds path for executable
  • Returns: string representing the full path to the exe
  • Args: none

🌸 new 🌸

  • Title: new
  • Usage: $rm->new(@params)
  • Function: creates a new Tmhmm factory
  • Returns: Bio::Tools::Run::Tmhmm
  • Args: (nothing listed)

💀 predict_protein_features 💀

  • Title: predict_protein_features()
  • Usage: DEPRECATED — use $obj->run($seq) instead
  • Function: Runs Tmhmm and creates an array of featrues
  • Returns: An array of Bio::SeqFeature::Generic objects
  • Args: A Bio::PrimarySeqI
🚨 Not me showing up to the party late — this one is deprecated, bestie. Use $obj->run($seq) instead. It's giving "old faithful but make it retired". 🙈

🧚 executable 🧚

  • Title: executable
  • Usage: my $exe = $tmhmm->executable('tmhmm');
  • Function: Finds the full path to the 'tmhmm' executable
  • Returns: string representing the full path to the exe
  • Args:
    • [optional] name of executable to set path to
    • [optional] boolean flag whether or not warn when exe is not found

🔥 run 🔥

  • Title: run()
  • Usage: $obj->run($seq)
  • Function: Runs Tmhmm and creates an array of featrues
  • Returns: An array of Bio::SeqFeature::Generic objects
  • Args: A Bio::PrimarySeqI

🙈 _input 🙈

  • Title: _input
  • Usage: obj->_input($seqFile)
  • Function: Internal (not to be used directly)
  • Returns: (nothing listed)
  • Args: (nothing listed)
🫶 the leading underscore means internal, so hands off, bestie — not for direct use.

🌈 _run 🌈

  • Title: _run
  • Usage: $obj->_run()
  • Function: Internal (not to be used directly)
  • Returns: An array of Bio::SeqFeature::Generic objects
  • Args: (nothing listed)

⭐ _writeSeqFile ⭐

  • Title: _writeSeqFile
  • Usage: obj->_writeSeqFile($seq)
  • Function: Internal (not to be used directly)
  • Returns: (nothing listed)
  • Args: (nothing listed)

and that's the whole page, bestie 💖✨ This little masterpiece is running on perl v5.36.0, dated 2023-01-22, and the page itself is Bio::T...:Tmhmm(3pm) from the User Contributed Perl Documentation. Periodt. 💅🎀

📦 where this page comes from