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

✨ NAME ✨

Bio::Coordinate::Utils 💖 the little helper class that makes Bio::Coordinate objects for you — like, your personal matchmaker but for coordinates.

It lives in the Bio::Coordinate::Utils corner of the Perl-verse (manual page: Bio::C...:Utils(3pm), User Contributed Perl Documentation, bestie 💅).

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🌸 VERSION 🌸

version 1.007001 — yeah she's got a version number and she's proud of it 🎀

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🦋 SYNOPSIS 🦋

use Bio::Coordinate::Utils;
# get a Bio::Align::AlignI compliant object, $aln, somehow
# it could be a Bio::SimpleAlign

$mapper = Bio::Coordinate::Utils->from_align($aln, 1);

# Build a set of mappers which will map, for each sequence,
# that sequence position in the alignment (exon position to alignment
# position)
my @mappers = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln);

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💜 DESCRIPTION 💜

Okay so picture this: this class is basically a holder — a cute little container — for methods that work on or create Bio::Coordinate::MapperI-compliant objects. That's the whole job. ✨

Real talk though: these methods are not part of the Bio::Coordinate::MapperI interface, and in general they should not be essential to the primary function of sequence objects. Like, they're the fun side quests, not the main plot.

So if you're sitting there thinking "hmm, should I add an essential function in here?" — maybe don't 🙈 it might genuinely be better to go make your own sequence class. See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq for more. iykyk.

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👑 METHODS 👑

🧚 new

new() inherited from Root — that's it, that's the whole vibe, she didn't need to reinvent anything 💅

🌈 from_align

• Title : from_align
• Usage : $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
• Function:
  • Create a mapper out of an alignment.
  • The mapper will return a value only when both ends of the input range find a match.
  • Note: This implementation works only on pairwise alignments and is not yet well tested!
• Returns : A Bio::Coordinate::MapperI
• Args :
  • Bio::Align::AlignI object
  • Id for the reference sequence, optional

⚠️ bestie listen — this one only does pairwise alignments, and she is not yet well tested. Proceed with the appropriate amount of caution, fr fr 😭

💖 from_seq_to_alignmentpos

• Title : from_seq_to_alignmentpos
• Usage : $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
• Function:
  • Create a mapper out of an alignment.
  • The mapper will map the position of a sequence into that position in the alignment.
  • Will work on alignments of >= 2 sequences
• Returns : An array of Bio::Coordinate::MapperI
• Args : Bio::Align::AlignI object

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📬 FEEDBACK 📬

💌 Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, your comments and suggestions are the glow-up fuel. Send them 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. Why? Because there are many experienced and responsive experts who will be able to look at the problem and quickly address it — a whole group chat of geniuses, basically. 👑

Please include a thorough description of the problem with code and data examples if at all possible. The more detail, the faster the slay. ✨

🐛 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

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🌟 AUTHORS 🌟

Heikki Lehvaslaiho <heikki@bioperl.org>

Jason Stajich <jason@bioperl.org>

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🎀 COPYRIGHT 🎀

This software is copyright (c) by Heikki Lehvaslaiho, and by Jason Stajich.

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

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And that's the whole page, bestie!! 💜 This was perl v5.32.0, dated 2020-11-24 — shoutout to the Bio::C...:Utils(3pm) manual for being iconic, no cap. Go map some coordinates, you absolute main character 🦋✨💅