Bio::Tools::Coil(3pm)

🧬 Bio::Tools::Coil — the manual, but make it cute

Bestie. You found the page for Bio::Tools::Coil, part of the User Contributed Perl Documentation crew. It's a parser for Coil output, and honestly? It just does its one little job and does it well. 💅

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✨ NAME ✨

Bio::Tools::Coil — parser for Coil output. That's it, that's the whole vibe. 🎀

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🌸 SYNOPSIS 🌸

okay so here's how you actually use it, copy-paste energy:

use Bio::Tools::Coil
my $parser = Bio::Tools::Coil->new();
while( my $sp_feat = $parser->next_result($file) ) {
      #do something
      #eg
      push @sp_feat, $sp_feat;
}

Make a parser, loop over results, push the features somewhere. Iconic. Slay. ✨

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💖 DESCRIPTION 💖

Parser for Coil output. Short. Sweet. To the point. She knows what she is. 🦋

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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, they mean it 🥹)

 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 more detail the better, bestie — they can't read your mind 💀)

🐛 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/bioperl-live/issues

No cap, if you found a bug, tell them. That's the whole point of a tracker. 🌈

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👑 AUTHOR 👑

Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil originally written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>

# Please direct questions and support issues to <bioperl-l@bioperl.org>
#

Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)

Shoutout to the whole lineage of people who kept this thing alive. Legends only. 🫶

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — so if you see an underscore, that's your lil "do not touch, this is behind the scenes" signal. 🙈

🔍 parse_results

• Title: parse_results
• Usage: obj->parse_results
• Function: Parses the coil output. Automatically called by next_result() if not yet done.
• Example:
• Returns:

➡️ next_result

• Title: next_result
• Usage:

while($feat = $coil->next_result($file)) {
         # do something
  }

• Function: Returns the next protein feature of the coil output file
• Returns:
• Args:

This is the one you'll be calling in a loop, bestie. Main character energy right here. ⭐

🫧 _result

• Title: _result
• Usage: $feat = $obj->_result()
• Function: internal
• Example:
• Returns:

🫧 _add_prediction

• Title: _add_prediction()
• Usage: $obj->_add_prediction($feat)
• Function: internal
• Example:
• Returns:

🫧 _predictions_parsed

• Title: _predictions_parsed
• Usage: $obj->_predictions_parsed
• Function: internal
• Example:
• Returns: TRUE or FALSE

🫧 create_feature

• Title: create_feature
• Usage: obj->create_feature(\%feature)
• Function: Internal(not to be used directly)
• Returns:
• Args:

🫧 _read_fasta

• Title: _read_fasta
• Usage: obj->_read_fasta($file)
• Function: Internal(not to be used directly)
• Returns:
• Args:

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That's the whole page, and yes, we made it to the end together. 🎀

This lil cutie was documented for perl v5.32.1 and stamped 2021-08-15 — so that's the version and date of this manual page, preserved with love. 💖

go parse some coils, bestie. you got this. ✨🦋🌸