Bio::S...WABAHSP(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 Bio::S...WABAHSP(3pm) 💖

okay bestie, welcome to the manual page for Bio::Search::HSP::WABAHSP — a User Contributed Perl Documentation situation, and yes it is exactly as niche and iconic as it sounds 💅

✨ NAME ✨

Bio::Search::HSP::WABAHSP — an HSP object that's built for describing WABA alignments. that's the whole vibe, that's the whole job 🦋

🌸 SYNOPSIS 🌸

# use this object as you would a GenericHSP # a few other methods have been
# added including state

no cap, that comment is doing a lot of heavy lifting for us here 😭

🎀 DESCRIPTION 🎀

so this object implements a few of the extra methods — like hmmstate_string, which hands you back the HMM state representation for the WABA alignment. slay.

we also must implement a method to calculate homology_string, because the algorithm simply does not return it in the machine readable format. so we do it ourselves. main character energy fr fr 👑

📬 FEEDBACK 📬

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, it's the whole glow-up process 🫶 send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated, periodt.

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. why? because many experienced and reponsive experts will be able look at the problem and quickly address it 💜

and bestie, please include a thorough description of the problem with code and data examples if at all possible. the more context the better, iykyk.

🐛 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

do it for the plot 🌈

👑 AUTHOR - Jason Stajich

email jason@bioperl.org

📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (so if you see an underscore, that's your cue that it's an inside-job method 🙈).

⭐ new

  • Title: new
  • Usage: my $obj = Bio::Search::HSP::WABAHSP->new();
  • Function: builds a new Bio::Search::HSP::WABAHSP object
  • Returns: Bio::Search::HSP::WABAHSP
  • Args: -hmmstate_seq => the string representing the state output from WABA

⭐ hmmstate_string

  • Title: hmmstate_string
  • Usage: my $hmmseq = $wabahsp->hmmstate_string();
  • Function: get/set the WABA HMM stateseq
  • Returns: string
  • Args: [optional] string

⭐ homology_string

  • Title: homolgy_string
  • Usage: my $homology_str = $hsp->homology_string();
  • Function: Homology string must be calculated for a WABA HSP so we can do so here and cache the result so it is only done once
  • Returns: string
  • Args: none
ngl the cached-once thing is lowkey the most thoughtful part of this whole page — nobody wants to recompute that 💀

that's the whole page bestie, hope it ate 💖

this page is running on perl v5.32.1 and is dated 2021-08-15 — a true vintage moment, vintage like a fine wine, obsessed 🍓

📦 where this page comes from