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

💖 NAME 💖

So bestie, this is the page for Bio::Search::HSP::HmmpfamHSP — a parser and HSP object for hmmpfam hsps. It ships with User Contributed Perl Documentation, and yes it's a Perl module page, we're doing this 💅

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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) {
                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
                        }
                }
    }

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🌸 DESCRIPTION 🌸

This object implements a parser for hmmpfam hsp output, which is a program in the HMMER package. That's the whole vibe. It parses, it objects, it serves 💅

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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 🥺

  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. (Yes, "reponsive" — that's the original typo and I'm not touching it, iconic of it honestly 💀)

🐛 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 _

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🎀 new 🎀

• Title : new
• Usage : my $obj = Bio::Search::HSP::HmmpfamHSP->new();
• Function: Builds a new Bio::Search::HSP::HmmpfamHSP object.
• Returns : Bio::Search::HSP::HmmpfamHSP
• Args :

          -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
          -parent => Bio::PullParserI object (required if no -chunk)
          -hsp_data => array ref with [rank query_start query_end hit_start
                                                                               hit_end score evalue]

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

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🌈 query 🌈

• Title : query
• Usage : my $query = $hsp->query
• Function: Returns a SeqFeature representing the query in the HSP
• Returns : L<Bio::SeqFeature::Similarity>
• Args : none

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⭐ hit ⭐

• Title : hit
• Usage : my $hit = $hsp->hit
• Function: Returns a SeqFeature representing the hit in the HSP
• Returns : L<Bio::SeqFeature::Similarity>
• Args : [optional] new value to set

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🧚 gaps 🧚

• Title : gaps
• Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
• Function : Get the number of gaps in the query, hit, or total alignment.
• Returns : Integer, number of gaps or 0 if none
• Args :
  • 'query' = num conserved / length of query seq (without gaps)
  • 'hit' = num conserved / length of hit seq (without gaps)
  • 'total' = num conserved / length of alignment (with gaps)
  • default = 'total'

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🍓 pvalue 🍓

• Title : pvalue
• Usage : my $pvalue = $hsp->pvalue();
• Function: Returns the P-value for this HSP
• Returns : undef (Hmmpfam reports do not have p-values)
• Args : none

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and that's the whole page bestie, no notes 💖✨🦋

This little legend was brought to you by perl v5.30.0, dated 2019-10-29, on page Bio::Search::HSP::HmmpfamHSP(3pm) — go parse something iconic, mwah 💅🎀