Bio::S...staHSP(3pm)

💖 Bio::Search::HSP::FastaHSP 💖

okay so bestie, this is a page from the User Contributed Perl Documentation collection, and it's all about Bio::Search::HSP::FastaHSP — the HSP object that carries around FASTA-specific data. yes, we're doing bioinformatics AND perl today. we contain multitudes. 🧬✨

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🌸 NAME 🌸

Bio::Search::HSP::FastaHSP — it's the HSP object for FASTA specific data. that's it, that's the name, no notes. 💅

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🦋 SYNOPSIS 🦋

the classic move: pull a FastaHSP out of a SearchIO stream, like so 👇

# get a FastaHSP from a SearchIO stream
my $in = Bio::SearchIO->new(-format => 'fasta', -file => 'filename.fasta');

while( my $r = $in->next_result) {
    while( my $hit = $r->next_result ) {
         while( my $hsp = $hit->next_hsp ) {
            print "smith-waterman score (if available): ",
                  $hsp->sw_score(),"\n";
         }
    }
}

nested while loops going three deep? it's giving archaeology dig but honestly it's the standard SearchIO walk. you go result → hit → hsp. 🫶

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✨ DESCRIPTION ✨

"Describe the object here"

yeah. that's the whole description. the module author left us a little sticky note and honestly? iconic. 😭 i'm not gonna invent lore that isn't there — the original literally just says to describe the object here. consider the object described. moving on. 💀

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📬 FEEDBACK 📬

💌 Mailing Lists

user feedback is, like, a whole pillar of how this module and the rest of the Bioperl modules evolve, and the devs genuinely want your thoughts and suggestions. participation is very much appreciated. send them to the Bioperl mailing list:

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

🛟 Support

important: send your usage questions and support issues to the mailing list

bioperl-l@bioperl.org

and not straight to the module maintainer's DMs (metaphorically speaking). there are lots of experienced and responsive experts on there who can look at your problem and sort it out fast. and pls include a thorough description of the problem, with code and data examples if at all possible — the more context, the better. ✨

🐛 Reporting Bugs

found a bug? report it to the Bioperl bug tracking system so they can keep track of what's broken and how it got fixed. bug reports go through the web here:

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

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👑 AUTHOR - Jason Stajich 👑

shoutout to Jason Stajich for writing this. email: jason-at-bioperl.org (you know the drill, swap the -at- for an @, anti-spam queen behavior). 💜

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📖 APPENDIX 📖

the rest of this documentation details every single object method, one by one. internal methods are usually prefixed with a _, so if you see that underscore you know it's an inside-job method. 🔍

🎀 new

• Title: new
• Usage: my $obj = Bio::Search::HSP::FastaHSP->new();
• Function: Builds a new Bio::Search::HSP::FastaHSP object
• Returns: Bio::Search::HSP::FastaHSP
• Args: -swscore => smith-waterman score

fresh object, just dropped. pass it the smith-waterman score via -swscore and you're off. 🌈

🎀 sw_score

• Title: sw_score
• Usage: $obj->sw_score($newval)
• Function: Get/Set Smith-Waterman score
• Returns: value of sw_score
• Args: newvalue (optional)

getter AND setter in one, the classic perl two-for-one. call it with no args to read the Smith-Waterman score, hand it a value to set one. ⭐

🎀 evalue2

• Title: evalue2
• Usage: $obj->evalue2($newval)
• Function: Get/Set E2() expectation value
• Returns: value of evalue2
• Args: newvalue (optional)

same energy, different stat: this one gets/sets the E2() expectation value. optional arg, so it flexes both ways. 🦋

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and that's the whole page, bestie — every method, every arg, every mailing list, nothing skipped. 🫶

this was written by perl v5.32.1, dated 2021-08-15, and it lives in the Bio::S...staHSP(3pm) corner of the manual. take care of her. 💅✨