Bio::A...::selex(3pm)

✨ NAME ✨

Bio::AlignIO::selex — it's a selex sequence input/output stream, bestie 💖

Like, it's the little translator that speaks fluent selex so you don't have to.

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🦋 SYNOPSIS 🦋

  # Do not use this module directly.  Use it via the L<Bio::AlignIO> class.

  use Bio::AlignIO;
  use strict;

  my $in = Bio::AlignIO->new(-format => 'selex',
                             -file   => 't/data/testaln.selex');
  while( my $aln = $in->next_aln ) {

  }

ok real talk — do NOT use this module directly. It's giving "I work best behind the scenes." You go through the Bio::AlignIO class, periodt 💅

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🌸 DESCRIPTION 🌸

This object can transform Bio::Align::AlignI objects to and from selex flat file databases. That's it, that's the whole job, and she does it beautifully ✨

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💌 FEEDBACK 💌

🫶 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Not me sending your whole life story to one person's inbox 🙈 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 more receipts the better, fr fr.

🐛 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:

  https://github.com/bioperl/bioperl-live/issues

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👑 AUTHORS - Peter Schattner 👑

Email: schattner@alum.mit.edu

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🌈 CONTRIBUTORS 🌈

Jason Stajich, jason-at-bioperl.org

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🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk, if you see that underscore, you're in the backstage area 🧚

⭐ next_aln

• Title : next_aln
• Usage : $aln = $stream->next_aln()
• Function: returns the next alignment in the stream. Tries to read all selex It reads all non whitespace characters in the alignment area. For selexs with weird gaps (eg ~~~) map them by using $al->map_chars('~','-')
• Returns : Bio::Align::AlignI object
• Args : NONE

ngl, the weird-gap thing is the plot twist. See a ~~~? Not a typo, not a vibe, that's a gap. Map it with $al->map_chars('~','-') and you're golden 🥰

💅 write_aln

• Title : write_aln
• Usage : $stream->write_aln(@aln)
• Function: writes the $aln object into the stream in selex format
• Returns : 1 for success and 0 for error
• Args : Bio::Align::AlignI object

one for the slay, zero for the nay 💀

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and that's the whole page, bestie!! this little icon is living in perl v5.32.1, dated 2021-08-15, and it's part of the Bio::A...::selex(3pm) situation — the one and only, User Contributed Perl Documentation core 🎀✨ go forth and parse, you absolute main character 🫶