Bio::T...ndrome(3pm)

💖 Bio::Tools::EMBOSS::Palindrome 💖

okay so bestie, welcome to Bio::T...ndrome(3pm) — this page lives in the User Contributed Perl Documentation section, and it's all about Bio::Tools::EMBOSS::Palindrome. no cap, it's a whole module. let's go ✨

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🌸 NAME 🌸

Bio::Tools::EMBOSS::Palindrome — parse EMBOSS palindrome output. that's the vibe. that's the job. 🎀

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🦋 SYNOPSIS 🦋

a simple script to turn palindrome output into GFF3:

# a simple script to turn palindrome output into GFF3
use Bio::Tools::EMBOSS::Palindrome;
use Bio::Tools::GFF;

my $parser = Bio::Tools::EMBOSS::Palindrome->new(-file => $filename);
my $out    = Bio::Tools::GFF->new(-gff_version => 3,
                                 -file => ">$filename.gff");
while( my $seq = $parser->next_seq ) {
   for my $feat ( $seq->get_SeqFeatures ) {
      $out->write_feature($feat);
   }
}

like… look at that. parser in, features out, GFF3 on disk. it's giving pipeline. 🔥

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👑 DESCRIPTION 👑

This is a parser for the EMBOSS tool palindrome. 💅 It will produce a Bio::Seq object for each sequence analyzed. The sequence will be empty (but will be of the correct length) and will have attached to it Bio::SeqFeature::FeaturePair objects which wil

okay so real talk, that sentence literally just ends at "which wil" in the original. i'm not gonna invent the rest, bestie, i'm just gonna leave it there lookin cute and mysterious 💀

🔮 FUTURE WORK 🔮

It may be consolidated into another framework at a later time, but for the time being it will stay a separate modules.

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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. (yes they mean you, specifically, babe 🌈)

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.

fr fr, the mailing list has the experts. the maintainer is right there but pls don't. 🙈

🐛 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 email or the web:

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

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🌟 AUTHOR - Jason Stajich 🌟

Email jason-at-bioperl-dot-org

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

🍓 new

• Title: new
• Usage: my $obj = Bio::Tools::EMBOSS::Palindrome->new();
• Function: Builds a new Bio::Tools::EMBOSS::Palindrome object
• Returns: an instance of Bio::Tools::EMBOSS::Palindrome
• Args: -file/-fh => a filename or filehandle for initializing the parser

⭐ next_seq

• Title: next_seq
• Usage: my $seq = $parser->next_seq;
• Function: Get the next feature set from the
• Returns: L<Bio::SeqI> object
• Args: none

and yes, "Get the next feature set from the" also just stops mid-thought in the original. two cliffhangers in one manpage, iconic behavior honestly 💀✨

🌈 source_tag

• Title: source_tag
• Usage: $obj->source_tag($newval)
• Function: Get/Set Source Tag ('palindrome') by default
• Returns: value of source_tag (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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and that's the whole page, bestie!! 💖 this was perl v5.32.1, dated 2021-08-15, straight from the Bio::T...ndrome(3pm) corner of the User Contributed Perl Documentation universe. go parse some palindromes, you absolute main character. periodt. 👑🦋🌸