Bio::C...ngPair(3pm)

💖 Bio::C...ngPair(3pm) — User Contributed Perl Documentation 💖

okay bestie, welcome to Bio::C...ngPair(3pm) — yes that's the whole name, it's giving mysterious, the manual page name is literally truncated like that and we're just gonna roll with it ✨

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🌸 NAME 🌸

Bio::Coordinate::ExtrapolatingPair — a continuous match between two coordinate sets. lowkey iconic.

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⭐ VERSION ⭐

version 1.007001 — periodt, that's the one.

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✨ SYNOPSIS ✨

here's the vibe in code, copy it exactly bestie:

use Bio::Location::Simple;
use Bio::Coordinate::ExtrapolatingPair;

$match1 = Bio::Location::Simple->new
  (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
$match2 = Bio::Location::Simple->new
  (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );

$pair = Bio::Coordinate::ExtrapolatingPair->
  new(-in => $match1,
      -out => $match2,
      -strict => 1
     );

$pos = Bio::Location::Simple->new
    (-start => 40, -end => 60, -strand=> 1 );
$res = $pair->map($pos);
$res->start eq 20;
$res->end eq 20;

like. it maps. it slays. that's the whole thing 🫶

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🦋 DESCRIPTION 🦋

so this class represents one continuous match between two coordinate systems, and those coordinate systems are represented by Bio::Location::Simple objects. the relationship is directed and reversible. it's got methods that keep the internal consistency in check, and it maps continuous and split locations from one coordinate system over to the other. very much main character energy 👑

this class is an elaboration of Bio::Coordinate::Pair. the map function returns only matches, which — no cap — is the mode you need most of the time. by default, the matching regions between the coordinate systems are boundless, so you can be like "okay the gene starts from here in the chromosomal coordinate system and then extends indefinitely in both directions" and that's just fine. but if you want your matching regions defined exactly, you can absolutely do that — just set strict() to true. your call, bestie 💅

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🎀 METHODS 🎀

💜 new

it's the constructor. that's the entry. that's all the deets we got, no extra lore, respect the mystery 🙈

💜 strict

Title   : strict
Usage   : $obj->strict(1);
Function: Set and read the strictness of the coordinate system.
Example :
Returns : value of input system
Args    : boolean

set it, read it, live your truth. it's a boolean, it's giving strictness of the coordinate system 🌸

💜 map

Title   : map
Usage   : $newpos = $obj->map($loc);
Function: Map the location from the input coordinate system
          to a new value in the output coordinate system.

          In extrapolating coordinate system there is no location zero.
          Locations are...
Example :
Returns : new location in the output coordinate system or undef
Args    : Bio::Location::Simple

not the description literally trailing off mid-sentence 😭 "Locations are..." bestie what ARE they. we may never know. anyway — takes a Bio::Location::Simple, gives you back a new location in the output coordinate system, or undef. and heads up: in the extrapolating coordinate system there is no location zero. no zero. it's not there. don't go looking 🔥

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🧚 INTERNAL METHODS 🧚

💜 _map

Title   : _map
Usage   : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called
          multiple times by map() if the location to be mapped is a
          split location

Example :
Returns : new location in the output coordinate system or undef
Args    : Bio::Location::Simple

this is the internal one, the behind-the-scenes girlie doing the actual mapping. map() calls it multiple times whenever the location you're mapping is a split location. she's not for you, she's for the machinery, but we stan her anyway ✨

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🌈 FEEDBACK 🌈

💌 Mailing lists

user feedback is an integral part of the evolution of this and other Bioperl modules — genuinely, it's a whole thing. send your comments and suggestions preferably to the Bioperl mailing list, and 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. like, don't DM the maintainer, post in the group chat bestie. many experienced and responsive experts will be able to look at the problem and quickly address it. and if at all possible, please include a thorough description of the problem with code and data examples — the more deets the better, fr fr 💅

💌 Reporting bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/%%7Bdist%7D

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👑 AUTHOR 👑

Heikki Lehvaslaiho <heikki@bioperl.org> — thank you for your service, king 🫡

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🌸 COPYRIGHT 🌸

this software is copyright (c) by Heikki Lehvaslaiho.

this software is available under the same terms as the perl 5 programming language system itself.

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and that's the page, bestie!! 💖 this one came from perl v5.32.0, dated 2020-11-24, and it lives in Bio::C...ngPair(3pm) — go forth and extrapolate responsibly 🦋✨💅