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

🌸 NAME 🌸

Bio::Search::Result::BlastPullResult — a parser and result object for BLASTN results 💖

(and yes bestie, this whole page is the manual for Bio::S...Result(3pm), from the User Contributed Perl Documentation ✨)

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🦋 SYNOPSIS 🦋

# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
                            -file   => 'result.blast');

while (my $result = $in->next_result) {
    print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
}

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🌈 DESCRIPTION 🌈

Okay so this object implements a parser for NCBI BLASTN result output. That's the whole vibe. It's giving glue between your raw BLASTN output and nice Perl objects 💅

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💌 FEEDBACK 💌

🎀 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. (fr fr, they mean it — y'all are the main character of this project's growth 🫶)

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

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

bestie pls do NOT slide into the maintainer's DMs with a support question, the mailing list is right there and it's full of geniuses 😭 include code and data examples, thorough description, all of it ✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us 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 - Sendu Bala 👑

Email bix@sendu.me.uk

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🌟 CONTRIBUTORS 🌟

Additional contributors names and emails here

not me reading the original and it literally says "Additional contributors names and emails here" 💀 that's a placeholder bestie, that's the actual text, I'm not making it up

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🔥 APPENDIX 🔥

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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🧚 new

• Title: new
• Usage: my $obj = Bio::SearchIO::Result::hmmpfam->new();
• Function: Builds a new Bio::SearchIO::Result::hmmpfam object
• Returns: Bio::SearchIO::Result::hmmpfam
• Args:
  • -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
  • -parent => Bio::PullParserI object (required if no -chunk)
  • -parameters => hash ref of search parameters (key => value), optional
  • -statistics => hash ref of search statistics (key => value), optional

where the array ref provided to -chunk contains an IO object for a filehandle to something representing the raw data of the result, and $start and $end define the tell() position within the filehandle that the result data starts and ends (optional; defaults to start and end of the entire thing described by the filehandle)

so like, you either hand it a -chunk or a -parent, pick one bestie, it's required either way 💅

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🦄 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

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🍓 hits

• Title: hits
• Usage: my @hits = $result->hits
• Function: Returns the HitI objects contained within this Result
• Returns: Array of Bio::Search::Hit::HitI objects
• Args: none

See Also: Bio::Search::Hit::HitI

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💜 sort_hits

• Title: sort_hits
• Usage: $result->sort_hits('<score')
• Function: Sorts the hits so that they come out in the desired order when hits() or next_hit() is called.
• Returns: n/a
• Args: A coderef for the sort function. See the documentation on the Perl sort() function for guidelines on writing sort functions.

By default the sort order is ascending significance value (ie. most significant hits first).

*** example

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🎀 rewind

• Title: rewind
• Usage: $result->rewind;
• Function: Allow one to reset the Hit iterator to the beginning, so that next_hit() will subsequently return the first hit and so on.
• Returns: n/a
• Args: none

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✨ get_statistic

• Title: get_statistic
• Usage: my $gap_ext = $result->get_statistic('kappa')
• Function: Returns the value for a specific statistic available from this result
• Returns: string
• Args: name of statistic (string)

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🌸 get_parameter

• Title: get_parameter
• Usage: my $gap_ext = $result->get_parameter('gapext')
• Function: Returns the value for a specific parameter used when running this result
• Returns: string
• Args: name of parameter (string)

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okay that's the whole page bestie, go parse some BLASTN results and slay 💅✨ this was perl v5.32.1, dated 2021-08-15, from the User Contributed Perl Documentation, Bio::S...Result(3pm) — mwah, take care of her 🫶🎀