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

Bio::Search::Hit::HmmpfamHit 💖

okay bestie, so this is the Bio::Search::Hit::HmmpfamHit page, part of the User Contributed Perl Documentation for Bio::S...famHit(3pm) — yes the man name is abbreviated like that, we don't make the rules 💅

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✨ NAME ✨

Bio::Search::Hit::HmmpfamHit — a parser and hit object for hmmpfam hits 🎀

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✨ SYNOPSIS ✨

ngl the usual move is to let Bio::SearchIO build these for you, like so:

    # 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) {
                while (my $hit = $result->next_hit) {
                        print $hit->name, "\n";
                        print $hit->score, "\n";
                        print $hit->significance, "\n";

                        while (my $hsp = $hit->next_hsp) {
                                # process HSPI objects
                        }
                }
    }

see how we're just vibing through results → hits → HSPs? it's giving very much main character energy 🌸

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✨ DESCRIPTION ✨

This object implements a parser for hmmpfam hit output, and hmmpfam is a program in the HMMER package. periodt. 🦋

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✨ FEEDBACK ✨

Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules — fr fr, they literally cannot grow without you 🫶. 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

...rather than to the module maintainer directly. Many experienced and responsive experts will be able to 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 — the more detail the better, bestie, they eat that up ✨

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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✨ APPENDIX ✨

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

new

Title   : new
Usage   : my $obj = Bio::Search::Hit::HmmpfamHit->new();
Function: Builds a new Bio::Search::Hit::HmmpfamHit object.
Returns : Bio::Search::Hit::HmmpfamHit
Args    : -chunk    => [Bio::Root::IO, $start, $end] (required if no -parent)
          -parent   => Bio::PullParserI object (required if no -chunk)
          -hit_data => array ref with [name description score significance
                                               num_hsps rank]

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

next_hsp

Title    : next_hsp
Usage    : while( $hsp = $obj->next_hsp()) { ... }
Function : Returns the next available High Scoring Pair
Example  :
Returns  : L<Bio::Search::HSP::HSPI> object or null if finished
Args     : none

note the Example line is empty in the original — iconic of it honestly, we respect the silence 💀

next_domain

Title   : next_domain
Usage   : my $domain = $hit->next_domain();
Function: An alias for L<next_hsp()>, this will return the next HSP
Returns : L<Bio::Search::HSP::HSPI> object
Args    : none

it's the same thing as next_hsp(), just wearing a different outfit 💅

hsps

Usage     : $hit_object->hsps();
Purpose   : Get a list containing all HSP objects.
Example   : @hsps = $hit_object->hsps();
Returns   : list of L<Bio::Search::HSP::BlastHSP> objects.
Argument  : none

domains

Title   : domains
Usage   : my @domains = $hit->domains();
Function: An alias for L<hsps()>, this will return the full list of hsps
Returns : array of L<Bio::Search::HSP::HSPI> objects
Args    : none

the full list, bestie, all of them 🌈

hsp

Usage     : $hit_object->hsp( [string] );
Purpose   : Get a single HSPI object for the present HitI object.
Example   : $hspObj  = $hit_object->hsp;  # same as 'best'
          : $hspObj  = $hit_object->hsp('best');
          : $hspObj  = $hit_object->hsp('worst');
Returns   : Object reference for a L<Bio::Search::HSP::HSPI> object.
Argument  : String (or no argument).
          :   No argument (default) = highest scoring HSP (same as 'best').
          :   'best'  = highest scoring HSP.
          :   'worst' = lowest scoring HSP.
Throws    : Exception if an unrecognized argument is used.

so basically: no arg or 'best' gets you the highest scoring HSP, 'worst' gets you the lowest scoring one, and if you pass something random it throws an exception at you 😭

See Also : hsps(), num_hsps()

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

it rewinds the Hit iterator back to the start so next_hit() starts handing out the first hit again — lowkey the rewind button of the hit world ⏪

strand

Usage     : $sbjct->strand( [seq_type] );
Purpose   : Gets the strand(s) for the query, sbjct, or both sequences.
          : For hmmpfam, the answers are always 1 (forward strand).
Example   : $qstrand = $sbjct->strand('query');
          : $sstrand = $sbjct->strand('hit');
          : ($qstrand, $sstrand) = $sbjct->strand();
Returns   : scalar context: integer '1'
          : array context without args: list of two strings (1, 1)
          : Array context can be "induced" by providing an argument of 'list'
                  : or 'array'.
Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default
          : = 'query') ('sbjct' is synonymous with 'hit')

for hmmpfam the answers are always 1 — forward strand, every single time, no plot twists 🌸

frac_aligned_query

Usage     : $hit_object->frac_aligned_query();
Purpose   : Get the fraction of the query sequence which has been aligned
          : across all HSPs (not including intervals between non-overlapping
          : HSPs).
Example   : $frac_alnq = $hit_object->frac_aligned_query();
Returns   : undef (the length of query sequences is unknown in Hmmpfam reports)
Argument  : none

heads up bestie: this one returns undef, because the length of query sequences is unknown in Hmmpfam reports 🙈

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and that's the whole page! this was Bio::S...famHit(3pm) from perl v5.30.0, dated 2019-10-29 — thanks for reading, mwah 💖🎀✨