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

💖 Bio::S...Result(3pm) 💖

okay bestie, welcome to the Bio::S...Result(3pm) page — a User Contributed Perl Documentation moment, brought to you by the Bioperl girlies. this one's all about Bio::Search::Result::BlastResult, and yes she is that girl. 🎀

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✨ NAME ✨

Bio::Search::Result::BlastResult — a Blast-specific subclass of Bio::Search::Result::GenericResult. it's giving inheritance, it's giving specialization, it's giving exactly what it says on the tin. 💅

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✨ SYNOPSIS ✨

    # Working with iterations (PSI-BLAST results)

    $result->next_iteration();
    $result->num_iterations();
    $result->iteration();
    $result->iterations();

# See Bio::Search::Result::GenericResult for information about working
with Results.

# See Bio::Search::Iteration::IterationI # for details about working
with iterations.

# TODO: #     * Show how to configure a SearchIO stream so that it
generates #       BlastResult objects.

heads up bestie: that # TODO: is still a todo. the docs are not yet showing you how to configure a SearchIO stream so that it generates BlastResult objects. we wait. 🙈

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✨ DESCRIPTION ✨

so this object is a subclass of Bio::Search::Result::GenericResult, and what she brings to the table is a lil extra something for working with BLAST and PSI-BLAST results. no cap. 🧚

for all the general "how do I even work with Results" tea, go read Bio::Search::Result::GenericResult. she's the main character, this one's the spin-off. 👑

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💌 FEEDBACK 💌

Mailing Lists

user feedback is literally an integral part of the evolution of this and other Bioperl modules — like, the whole ecosystem thrives on it. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated. 🫶

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 straight to the module maintainer, okay? (yes, the original spells it "reponsive" — we're keeping that energy, typo and all 💀). there are so many experienced and responsive experts on the list who will be able to look at the problem and quickly address it. please include a thorough description of the problem, plus code and data examples, if at all possible. the more detail the better, fr fr. 🌸

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

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🌟 AUTHOR - Steve Chervitz 🌟

Email sac@bioperl.org

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, that underscore is the "don't touch unless you know what you're doing" signal ✨).

new

• Title — new
• Usage — my $obj = Bio::Search::Result::BlastResult->new();
• Function — builds a new Bio::Search::Result::BlastResult object 🎀
• Returns — Bio::Search::Result::BlastResult
• Args — see Bio::Search::Result::GenericResult();

the following parameters are specific to BlastResult:

• -iterations => array ref of Bio::Search::Iteration::IterationI objects
• -inclusion_threshold => e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp)

hits

• Title — hits
• Usage — my @hits = $result->hits
• Function — returns the available hits for this Result
• Returns — Array of L<Bio::Search::Hit::HitI> objects
• Args — none
• Note — this method overrides L<Bio::Search::Result::GenericResult::hits> to take into account the possibility of multiple iterations, as occurs in PSI-BLAST reports.

if there are multiple iterations, all 'new' hits for all iterations are returned. these are the hits that did not occur in a previous iteration. new hits only, bestie. 💅

• See Also — L<Bio::Search::Result::GenericResult::hits>

next_hit

• Title — next_hit
• Usage — while( $hit = $result->next_hit()) { ... }
• Function — returns the next available Hit object, representing potential matches between the query and various entities from the database.
• Returns — a Bio::Search::Hit::HitI object or undef if there are no more.
• Args — none
• Note — this method overrides L<Bio::Search::Result::GenericResult::next_hit> to take into account the possibility of multiple iterations, as occurs in PSI-BLAST reports.

if there are multiple iterations, calling next_hit() traverses all of the hits, old and new, for each iteration, calling next_hit() on each iteration. she's thorough like that. 👑

• See Also — L<Bio::Search::Iteration::GenericIteration::next_hit>

num_hits

• Title — num_hits
• Usage — my $hitcount= $result->num_hits
• Function — returns the number of hits for this query result
• Returns — integer
• Args — none
• Note — this method overrides L<Bio::Search::Result::GenericResult::num_hits> to take into account the possibility of multiple iterations, as occurs in PSI-BLAST reports.

if there are multiple iterations, calling num_hits() returns the number of 'new' hits for each iteration. these are the hits that did not occur in a previous iteration.

• See Also — L<Bio::Search::Result::GenericResult::num_hits>

add_hit

• Title — add_hit
• Usage — $report->add_hit($hit)
• Function — adds a HitI to the stored list of hits
• Returns — number of HitI currently stored
• Args — Bio::Search::Hit::HitI

add_iteration

• Title — add_iteration
• Usage — $report->add_iteration($iteration)
• Function — adds a IterationI to the stored list of iterations
• Returns — number of IterationI currently stored
• Args — Bio::Search::Iteration::IterationI

next_iteration

• Title — next_iteration
• Usage — while( $it = $result->next_iteration()) { ... }
• Function — returns the next Iteration object, representing all hits found within a given PSI-Blast iteration.
• Returns — a Bio::Search::Iteration::IterationI object or undef if there are no more.
• Args — none

iteration

• Usage — $iteration = $blast->iteration( $number );
• Purpose — get an IterationI object for the specified iteration in the search result (PSI-BLAST).
• Returns — Bio::Search::Iteration::IterationI object
• Throws — Bio::Root::NoSuchThing exception if $number is not within range of the number of iterations in this report. so don't go asking for iteration 47 when there are three, bestie. 😭
• Argument — integer (optional, if not specified get the last iteration). first iteration = 1

num_iterations

• Usage — $num_iterations = $blast->num_iterations;
• Purpose — get the number of iterations in the search result (PSI-BLAST).
• Returns — total number of iterations in the report
• Argument — none (read-only)

number_of_iterations

• Usage — $num_iterations = $blast->number_of_iterations;
• Purpose — get the number of iterations in the search result (PSI-BLAST).
• Returns — total number of iterations in the report
• Argument — none (read-only)
• Note — alias of L<num_iterations>. same girl, different name. 💅

round

• Usage — $round = $blast->round( $number );
• Purpose — get an IterationI object for the specified iteration in the search result (PSI-BLAST).
• Returns — Bio::Search::Iteration::IterationI object
• Throws — Bio::Root::NoSuchThing exception if $number is not within range of the number of iterations in this report.
• Argument — integer (optional, if not specified get the last iteration). first iteration = 1
• Note — alias of L<iteration>.

iterations

• Title — iterations
• Usage — my @iterations = $result->iterations
• Function — returns the IterationI objects contained within this Result
• Returns — Array of L<Bio::Search::Iteration::IterationI> objects
• Args — none

psiblast

• Usage — if( $blast->psiblast ) { ... }
• Purpose — set/get a boolean indicator whether or not the report is a PSI-BLAST report.
• Returns — 1 if PSI-BLAST, undef if not.
• Argument — 1 (when setting)

no_hits_found

• Usage — $nohits = $blast->no_hits_found( $iteration_number );
• Purpose — get boolean indicator indicating whether or not any hits were present in the report.

this is NOT the same as determining the number of hits via the hits() method, which will return zero hits if there were no hits in the report or if all hits were filtered out during the parse.

thus, this method can be used to distinguish these possibilities for hitless reports generated when filtering. 🦋

• Returns — Boolean
• Argument — (optional) integer indicating the iteration number (PSI-BLAST). if iteration number is not specified and this is a PSI-BLAST result, then this method will return true only if all iterations had no hits found.

set_no_hits_found

• Usage — $blast->set_no_hits_found( $iteration_number );
• Purpose — set boolean indicator indicating whether or not any hits were present in the report.
• Returns — n/a
• Argument — (optional) integer indicating the iteration number (PSI-BLAST)

_next_iteration_index

• Title — _next_iteration_index
• Usage — private 🙈

rewind

• Title — rewind
• Usage — $result->rewind;
• Function — allow one to reset the Iteration iterator to the beginning. since this is an in-memory implementation.
• Returns — none
• Args — none

inclusion_threshold

• Title — inclusion_threshold
• Usage — my $incl_thresh = $result->inclusion_threshold; (read-only)
• Function — gets the e-value threshold for inclusion in the PSI-BLAST score matrix model (blastpgp) that was used for generating the report being parsed.
• Returns — number (real) or undef if not a PSI-BLAST report.
• Args — none

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and that's the whole page, bestie!! 💖✨🎀

this iconic lil slice of User Contributed Perl Documentation is perl v5.32.1, dated 2021-08-15. go forth and parse those BLAST results, you absolute legend. 🦋👑💅