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

💖 NAME 💖

Bio::Search::Result::HmmpfamResult — it's a parser and a result object, specifically for hmmpfam output. Two jobs, one icon. 💅

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✨ SYNOPSIS ✨

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

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

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🌸 DESCRIPTION 🌸

Bestie, listen. This object is a parser for hmmpfam result output — and hmmpfam is a program that lives inside the HMMER package. That's the whole vibe. 🦋

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

User feedback is, like, an integral part of the evolution of this module and all the other Bioperl modules. So if you have comments or suggestions, send them — preferably to the Bioperl mailing list. Your participation is so appreciated, fr fr. 😭

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

🎀 Support 🎀

Please send your usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

…and not straight to the module maintainer. The way that so many experienced and responsive experts hang out on that list means someone will look at your problem and address it fast. 💫 Please include a thorough description of the problem, with code and data examples, if at all possible. Give them the whole story, not just the cliffnotes. 🙈

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system — that's how we keep track of the bugs and their resolutions. 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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🌈 APPENDIX 🌈

The rest of the documentation goes deep on each of the object methods. Heads up: internal methods are usually preceded with a _. iykyk. 💀

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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)

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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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🌟 next_model 🌟

Title : next_model Usage : my $domain = $result->next_model Function: Returns the next domain — this is an alias for next_hit() Returns : L<Bio::Search::Hit::HitI> object 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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🌟 models 🌟

Title : models Usage : my @domains = $result->models; Function: Returns the list of HMM models seen — this is an alias for hits() Returns : Array of L<Bio::Search::Hit::HitI> objects Args : none

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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.

You will be sorting array references, not HitI objects. The
references contain name as element 0, description as element 1,
score as element 2, significance as element 3 and number of hsps
as element 4.
By default the sort order is ascending significance value (ie.
most significant hits first).

Note : To access the special variables $a and $b used by the Perl sort() function the user function must access Bio::Search::Result::HmmpfamResult namespace.

For example, use :

$result->sort_hits(
                  sub{$Bio::Search::Result::HmmpfamResult::a->[2]
                                           <=>
                          $Bio::Search::Result::HmmpfamResult::b->[2]});

NOT $result->sort_hits($a->[2] <=> $b->[2]);

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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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and that's the whole page, bestie!! 🎀 This was perl v5.30.0, dated 2019-10-29, and it lives under the name Bio::S...Result(3pm). Go parse some hmmpfam results, you absolute icon. 💅✨🦋