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

💖 NAME 💖

okay so bestie, welcome to Bio::A...istics(3pm) — a User Contributed Perl Documentation page, no cap — and the module it's serving is Bio::Align::PairwiseStatistics: the base statistic object for Pairwise Alignments. that's the whole name. iconic. periodt. ✨

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🦋 SYNOPSIS 🦋

use strict;
my $stats = Bio::Align::PairwiseStatistics->new();

# get alignment object of two sequences somehow
my $pwaln;
print $stats->number_of_comparable_bases($pwaln);
my $score = $stats->score_nuc($pwaln);

yes the # get alignment object of two sequences somehow comment is doing a lot of heavy lifting there and honestly? relatable. you get the alignment object however you get it, i believe in you 🫶

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🌸 DESCRIPTION 🌸

Calculate pairwise statistics.

that's it. that's the description. short, sweet, main character energy, we love a low-effort high-impact moment 💅

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💬 FEEDBACK 💬

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. send your comments and suggestions preferably to the Bioperl mailing list, and know that your participation is much appreciated. you showing up matters, bestie 🥹

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

🫶 Support

okay so for usage questions and support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, please and thank you 🙈 this way a whole crowd of experienced and responsive experts can look at your problem and address it fast. and when you write in, include a thorough description of the problem with code and data examples if at all possible — the more context you give, the more likely someone swoops in and fixes your whole life. no gatekeeping, just good bug reports ✨

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so everybody can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

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👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl-dot-org

(not me protecting the email from spam bots with the whole "at" and "dot" thing — a legend, truly 🎀)

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📚 APPENDIX 📚

the rest of the documentation goes into detail on each of the object methods. heads up: internal methods are usually preceded with a _ — so if you see an underscore, that's the secret menu, iykyk 👀

🧮 number_of_comparable_bases

• Title: number_of_comparable_bases
• Usage: my $bases = $stat->number_of_comparable_bases($aln);
• Function: returns the count of the number of bases that can be compared (L) in this alignment (length - gaps)
• Returns: integer
• Args: Bio::Align::AlignI

🔢 number_of_differences

• Title: number_of_differences
• Usage: my $nd = $stat->number_of_distances($aln);
• Function: returns the number of differences between two sequences
• Returns: integer
• Args: Bio::Align::AlignI

yes the Usage line literally says number_of_distances while the Title says number_of_differences. i am simply the messenger, copying it exactly as written, don't come for me 💀

🕳️ number_of_gaps

• Title: number_of_gaps
• Usage: my $nd = $stat->number_of_gaps($aln);
• Function: returns the number of gapped positions among sequences in alignment
• Returns: integer
• Args: Bio::Align::AlignI

🌟 score_nuc

• Title: score_nuc
• Usage:

my $score = $stat->score_nuc($aln);
  or
my $score = $stat->score_nuc(
  -aln =>$aln,
  -match    => 1,
  -mismatch => -1,
  -gap_open => -1,
  -gap_ext  => -1
);

• Function: calculate the score of an alignment of 2 nucleic acid sequences. the scoring parameters can be specified. otherwise the blastn default parameters are used: match = 2, mismatch = -3, gap opening = -5, gap extension = -2
• Returns: alignment score (number)
• Args: Bio::Align::AlignI, match score [optional], mismatch score [optional], gap opening score [optional], gap extension score [optional]

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and that's the whole page, bestie!! 💖✨🎀🦋🌸💅🫶

this lil masterpiece shipped as part of perl v5.32.1, dated 2021-08-15 — vintage, lowkey, and still eating. go forth and calculate those pairwise statistics, you absolute icon 👑🌈⭐