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

💖 NAME 💖

Bio::Search::Hit::BlastHit — the BLAST-specific subclass of Bio::Search::Hit::GenericHit, bestie 💅

Like... this is the page for Bio::S...astHit(3pm) and it's giving "GenericHit but make it BLAST." Periodt.

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✨ SYNOPSIS ✨

use Bio::Search::Hit::BlastHit;
my $hit = Bio::Search::Hit::BlastHit->new(-algorithm => 'blastp');

okay so that's the whole vibe right there 🫶

# See Bio::Search::Hit::GenericHit for information about working with
# Hits.

# TODO: Describe how to configure a SearchIO stream so that it generates
#       GenericHit objects.

ngl that TODO is literally still sitting there 😭 not me pointing at it. It is what it is. The docs just haven't been written yet, fr fr.

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🌸 DESCRIPTION 🌸

So this object is a subclass of Bio::Search::Hit::GenericHit, and what it does is provide some operations that make working with BLAST and PSI-BLAST Hits way easier. Obsessed with her honestly 💖

And if you want the general tea on working with Hits in general? Go read Bio::Search::Hit::GenericHit. She's the main character, this one is the spinoff. 👑

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🦋 FEEDBACK 🦋

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, the whole thing literally grows because of y'all 🫶 Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated, no cap.

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

...and NOT to the module maintainer directly, bestie, I'm begging 🙈 There are lots of experienced and reponsive experts who will be able to look at the problem and quickly address it. If at all possible, please include a thorough description of the problem with code and data examples — like, the full lore, not just "it doesn't work" 💀

🐛 Reporting Bugs

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

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

slay, an actual issue tracker. Use it 💅

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👑 AUTHOR - Jason Stajich and Steve Chervitz 👑

Email jason@bioperl.org Email sac@bioperl.org

Icons. Both of them. Periodt. 🎀✨

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — that underscore is basically the "backstage pass, do not touch" marker, iykyk 🤫

🌟 new

Title   : new
Usage   : my $obj = Bio::Search::Hit::GenericHit->new();
Function: Builds a new Bio::Search::Hit::GenericHit object
Returns : Bio::Search::Hit::GenericHit
Args    : See Bio::Search::Hit::GenericHit() for other args.
          Here are the BLAST-specific args that can be used when
          creating BlastHit objects:
          -iteration    => integer for the PSI-Blast iteration number
          -found_again  => boolean, true if hit appears in a
                           "previously found" section of a PSI-Blast report.

So yeah, new builds you a brand new object, it hands you back a Bio::Search::Hit::GenericHit, and for the other args you go check Bio::Search::Hit::GenericHit(). But these two are the BLAST-specific ones you can pass when you're creating BlastHit objects:

• -iteration — an integer for the PSI-Blast iteration number
• -found_again — a boolean, true if the hit appears in a "previously found" section of a PSI-Blast report

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🧚 iteration

Usage     : $hit->iteration( $iteration_num );
Purpose   : Gets the iteration number in which the Hit was found.
Example   : $iteration_num = $sbjct->iteration();
Returns   : Integer greater than or equal to 1
            Non-PSI-BLAST reports will report iteration as 1, but this number
            is only meaningful for PSI-BLAST reports.
Argument  : iteration_num (optional, used when setting only)
Throws    : none

See Also   : found_again()

She tells you which iteration the Hit was found in. The number you get back is an integer >= 1. Important caveat though: non-PSI-BLAST reports will just report iteration as 1, and honestly that number is only meaningful for PSI-BLAST reports — for everything else it's just kinda there for the vibe 🌸 The iteration_num argument is optional and it's only used when you're setting. Throws nothing. Chillest method alive.

Also go peep found_again() while you're here 💖

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💀 found_again

Title     : found_again
Usage     : $hit->found_again;
            $hit->found_again(1);
Purpose   : Gets a boolean indicator whether or not the hit has
            been found in a previous iteration.
            This is only applicable to PSI-BLAST reports.

             This method indicates if the hit was reported in the
             "Sequences used in model and found again" section of the
             PSI-BLAST report or if it was reported in the
             "Sequences not found previously or not previously below threshold"
             section of the PSI-BLAST report. Only for hits in iteration > 1.

Example   : if( $hit->found_again()) { ... };
Returns   : Boolean, true (1) if the hit has been found in a
            previous PSI-BLAST iteration.
            Returns false (0 or undef) for hits that have not occurred in a
            previous PSI-BLAST iteration.
Argument  : Boolean (1 or 0). Only used for setting.
Throws    : none

See Also   : iteration()

This one gives you a boolean telling you whether or not the hit has been found in a previous iteration. And heads up — this is only applicable to PSI-BLAST reports, so don't come for her with anything else 🙈

Here's the actual tea: this method indicates if the hit was reported in the "Sequences used in model and found again" section of the PSI-BLAST report, or if it was reported in the "Sequences not found previously or not previously below threshold" section of the PSI-BLAST report. Only for hits in iteration > 1. 🎯

So you get back a boolean: true (1) if the hit has been found in a previous PSI-BLAST iteration, and false (0 or undef) for hits that have not occurred in a previous PSI-BLAST iteration. The Argument is a boolean (1 or 0) and it's only used for setting. Throws nothing, ever. 👑

And obviously, go check iteration() too — they're a matched set, your honor 💅

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and that's the whole page, bestie!! 🫶✨ this was Bio::S...astHit(3pm), brought to you by perl v5.32.1 and dated 2021-08-15 — yes she's vintage, yes she still slays, no cap 💖🎀🦋 go read Bio::Search::Hit::GenericHit next, ily, bye!! 👑