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

👑 Bio::T...Signalp(3pm) — aka Bio::Tools::Signalp 💅

okay bestie, gather round, because this is the parser for Signalp output and it's genuinely so useful. it lives in the User Contributed Perl Documentation corner of the perl universe and yes, we're gonna read the whole thing together. no skimming. i'll know. 🙈

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✨ NAME ✨

Bio::Tools::Signalp — a parser for Signalp output. that's the whole name. short, sweet, iconic. periodt. 💖

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🦋 SYNOPSIS 🦋

here's the vibe, fr fr:

use Bio::Tools::Signalp;

my $parser = Bio::Tools::Signalp->new(-fh =>$filehandle );

while( my $sp_feat = $parser->next_result ) {
  if ($sp_feat->score > 0.9) {
     push @likely_sigpep, $sp_feat;
  }
}

see how easy that is?? you make a parser, you loop over results, you filter by score. main character energy. 🌸

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🎀 DESCRIPTION 🎀

so "SignalP" predicts the presence and location of signal peptide cleavage sites in amino acid sequences. that's its whole thing. it's very good at it.

Bio::Tools::Signalp parses the output of "SignalP" and hands you back a Bio::SeqFeature::Generic object describing the signal peptide it found, if any. if there isn't one? no feature, no drama. 🫶

it also returns a whole variety of tags extracted from the NN and HMM analysis. and the one you actually care about, the headliner, the queen:

the "score()" attribute contains the NN probability of this being a true signal peptide. 👑

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💬 FEEDBACK 💬

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, bestie. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated, like genuinely, we love to see 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. the reason is that many experienced and reponsive experts will be able look at the problem and quickly address it. (yes that's how the original spells "responsive", i am not touching it, it's part of the lore now 💀)

and please include a thorough description of the problem with code and data examples if at all possible. give us the full context, the whole story, the receipts. 📝

🐛 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 va the web:

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

(again: "va", not "via". i'm just the messenger. 🙈)

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🌟 AUTHOR 🌟

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

based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written by Marc Sohrmann (ms2_AT_sanger.ac.uk). written in BioPipe by Balamurugan Kumarasamy savikalpa_AT_fugu-sg.org. cared for by the Fugu Informatics team (fuguteam_AT_fugu-sg.org). 🧚

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💜 CONTRIBUTORS 💜

• Torsten Seemann — torsten.seemann AT infotech.monash.edu.au

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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 sign it's not for you, it's the module's own business. 🚫

🔧 new

• Title: new
• Usage: my $obj = Bio::Tools::Signalp->new();
• Function: Builds a new Bio::Tools::Signalp object
• Returns: Bio::Tools::Signalp
• Args: -fh/-file => $val, # for initing input, see Bio::Root::IO

🔧 next_result

• Title: next_result
• Usage: my $feat = $signalp->next_result
• Function: Get the next result set from parser data
• Returns: Bio::SeqFeature::Generic
• Args: none

🔧 _parse_hmm_result

• Title: _parse_hmm_result
• Usage: $self->_parse_hmm_result(\%feature)
• Function: Internal (not to be used directly)
• Returns: hash of feature values
• Args: hash of more feature values

🔧 _create_feature

• Title: _create_feature
• Usage: $self->create_feature(\%feature)
• Function: Internal (not to be used directly)
• Returns: hash of feature values
• Args: hash of more feature values

🔧 _seqname

• Title: _seqname
• Usage: $self->_seqname($name)
• Function: Internal (not to be used directly)
• Returns:
• Args:

🔧 _fact1

• Title: _fact1
• Usage: $self->fact1($fact1)
• Function: Internal (not to be used directly)
• Returns:
• Args:

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and that's the whole page, bestie!! 💖 this doc came to you courtesy of perl v5.32.1 and it's dated 2021-08-15. slay, go parse some signal peptides, you've got this. 🦋✨👑