Bio::T...o::Gerp(3pm)

👑 Bio::Tools::Phylo::Gerp(3pm) 👑

okay bestie, welcome to the Bio::Tools::Phylo::Gerp page — this is the Perl doc for the GERP-output parser, and we're gonna get you fluent in it. 🧬✨

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🌸 NAME 🌸

Bio::Tools::Phylo::Gerp — it parses output from GERP. that's the whole vibe. 🫶

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✨ SYNOPSIS ✨

here's the little ritual you do to make it work, no cap:

  use strict;

  use Bio::Tools::Phylo::Gerp;

  my $parser = Bio::Tools::Phylo::Gerp->new(-file => "alignment.rates.elems");

  while (my $feat = $parser->next_result) {
    my $start = $feat->start;
    my $end = $feat->end;
    my $rs_score = $feat->score;
    my $p_value = ($feat->annotation->get_Annotations('p-value'))[0]->value;
  }

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💖 DESCRIPTION 💖

so this module's whole job is parsing the output from 'GERP' (v2), which was written by Eugene Davydov (and originally Gregory M. Cooper et al.). you can get all the deets here, bestie:

http://mendel.stanford.edu/sidowlab/

it works on the .elems files that gerpelem produces. 🍓

and every single result? it's a Bio::SeqFeature::Annotated representing one single constrained element. iconic behavior honestly. 👑

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🦋 FEEDBACK 🦋

💌 Mailing Lists 💌

user feedback is, like, integral to the evolution of this and other Bioperl modules — the way that your comments and suggestions actually shape things?? send them, preferably to the Bioperl mailing list. your participation is much appreciated, fr fr.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫶 Support 🫶

please direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, okay? there are so many experienced and reponsive experts there who'll be able to look at your problem and quickly address it. please include a thorough description of the problem, plus code and data examples if at all possible. the more context you give, the faster someone can help. 💅

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system so we can actually keep track of them and their resolutions — it's giving organized. bug reports can be submitted via the web:

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

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🌈 AUTHOR - Sendu Bala 🌈

Email bix@sendu.me.uk

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🎀 APPENDIX 🎀

the rest of the documentation goes into the details of each of the object methods. just so you know: internal methods are usually preceded with a _. 🙈

⭐ new ⭐

  Title   : new
  Usage   : my $obj = Bio::Tools::Phylo::Gerp->new();
  Function: Builds a new Bio::Tools::Phylo::Gerp object
  Returns : Bio::Tools::Phylo::Gerp
  Args    : -file (or -fh) should contain the contents of a gerpelem .elems file

so new builds you a brand-new Bio::Tools::Phylo::Gerp object, and it hands one right back to you. 💖 the args: -file (or -fh) should contain the contents of a gerpelem .elems file.

⭐ next_result ⭐

  Title   : next_result
  Usage   : $result = $obj->next_result();
  Function: Returns the next result available from the input, or undef if there
            are no more results.
  Returns : Bio::SeqFeature::Annotated object. Features are annotated with a tag
            for 'pvalue', and a 'predicted' tag. They have no sequence id unless
            the input GERP file is non-standard, with the seq id as the 6th
            column.

            NB: feature coordinates are alignment columns of the alignment
            used to create the result file.
  Args    : none

next_result gives you the next result available from the input, or undef once there are no more results. simple as that. ✨

what you get back is a Bio::SeqFeature::Annotated object. these features are annotated with a tag for 'pvalue', plus a 'predicted' tag. they have no sequence id — unless the input GERP file is non-standard and has the seq id as the 6th column.

NB: feature coordinates are alignment columns of the alignment used to create the result file. don't forget that part, bestie, it matters. 😭

args: none. 💅

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perl v5.32.1 · 2021-08-15 · that's the source/version-and-date energy, and that's a wrap on this page 🎀💜 slay, go parse some constrained elements, and remember: the facts don't change, only the vibe. periodt. 🦋✨