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

💖 Bio::C...:Result(3pm) — the group-chat guide 💖

okay bestie, so you've found yourself in the Bio::C...:Result(3pm) page (that's Bio::Coordinate::Result in the Bioperl docs, the name got a lil truncated by the man renderer, we love her anyway ✨). She's a User Contributed Perl Documentation page and she is so important. let's get into it.

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✨ NAME ✨

Bio::Coordinate::Result — Results from coordinate transformation. that's it, that's the whole job 🎀

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🌸 VERSION 🌸

version 1.007001 — she's got a version, she's official 💅

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🦋 SYNOPSIS 🦋

  use Bio::Coordinate::Result;

  #get results from a Bio::Coordinate::MapperI
  $matched = $result->each_match;

literally just import her and start pulling matches out. no cap. 🔥

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💜 DESCRIPTION 💜

so when a Bio::Coordinate::MapperI does its thing, the results get kept in an object — and plot twist — that object is itself a split location. see Bio::Location::Split for the deets, iykyk.

the results you get back are either Matches or Gaps. go look at Bio::Coordinate::Result::Match and Bio::Coordinate::Result::Gap for those.

and here's the convenient part: if only one Match comes back, there's a convenience method for retrieving it or for accessing its methods directly. same energy for a Gap. bestie that's so thoughtful of her 🫶

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⭐ ATTRIBUTES ⭐

🌈 seq_id

Title   : seq_id
Usage   : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to

          We override this here in order to propagate to all sublocations
          which are not remote (provided this root is not remote either)

Returns : seq_id
Args    : [optional] seq_id value to set

so we're overriding this one here specifically so the value propagates down to all the sublocations that aren't remote — as long as this root isn't remote either. read that clause twice, it matters 👑

🌸 each_gap

Title   : each_gap
Usage   : $obj->each_gap();
Function:

          Returns a list of Bio::Coordianate::Result::Gap objects.

Returns : list of gaps
Args    : none

(yes the original says Bio::Coordianate::Result::Gap, typo and all, we're preserving her exactly 💀) no args, just vibes, get your list of gaps.

🎀 each_match

Title   : each_match
Usage   : $obj->each_match();
Function:

          Returns a list of Bio::Coordinate::Result::Match objects.

Returns : list of Matchs
Args    : none

returns a list of Matchs (pluralized her way, iconic), takes no args.

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💅 METHODS 💅

🦋 add_location

Title   : add_sub_Location
Usage   : $obj->add_sub_Location($variant)
Function:

          Pushes one Bio::LocationI into the list of variants.

Example :
Returns : 1 when succeeds
Args    : Location object

note the Title says add_sub_Location — capital L, that's not a typo I made, that's canon. push a Bio::LocationI onto the variants list, get 1 back when it succeeds. ✨

💜 add_result

Title   : add_result
Usage   : $obj->add_result($result)
Function: Adds the contents of one Bio::Coordinate::Result
Example :
Returns : 1 when succeeds
Args    : Result object

takes a Result object, absorbs its contents, returns 1 when it works. merged, periodt.

⭐ match

Title   : match
Usage   : $match_object = $obj->match(); #or
          $gstart = $obj->gap->start;
Function: Read only method for retrieving or accessing the match object.
Returns : one Bio::Coordinate::Result::Match
Args    :

read-only, no args, hands you one Bio::Coordinate::Result::Match. (yes the usage example line shows $gstart = $obj->gap->start; under match — that's what the original says, keep it, we don't fix what we weren't asked to fix 🙈)

🌸 gap

Title   : gap
Usage   : $gap_object = $obj->gap(); #or
          $gstart = $obj->gap->start;
Function: Read only method for retrieving or accessing the gap object.
Returns : one Bio::Coordinate::Result::Gap
Args    :

read-only, no args, hands you one Bio::Coordinate::Result::Gap. the twin sister of match, we stan a matched set 👑

🎀 purge_gaps

Title   : purge_gaps
Usage   : $gap_count = $obj->purge_gaps;
Function: remove all gaps from the Result
Returns : count of removed gaps
Args    :

removes all the gaps from the Result and tells you how many she removed. spring cleaning energy, love that for her 🧹💖

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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, fr fr.

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.

(the original says "reponsive", not "responsive" — I'm keeping it exactly as written, no cap 💀)

🐛 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/%%7Bdist%7D

(and yes, %%7Bdist%7D is literally what's printed there. it's giving template variable that never got expanded, but it's her template variable 🌈)

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👑 AUTHOR 👑

Heikki Lehvaslaiho <heikki@bioperl.org>

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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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okay that's the whole page bestie, you're fully caught up, go forth and transform those coordinates 💖✨🦋

this was Bio::C...:Result(3pm) from perl v5.32.0, dated 2020-11-24 — and that's the sign-off, mwah 💅🎀