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

💖 NAME 💖

Bio::SearchIO::hmmer_pull — bestie, it's a parser for HMMER output ✨

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🌸 SYNOPSIS 🌸

# do not use this class directly it is available through Bio::SearchIO
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
                            -file   => 't/data/hmmpfam.bigout');
while (my $result = $in->next_result) {
    # this is a Bio::Search::Result::HmmpfamResult object
    print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
    while (my $hit = $result->next_hit) {
        print $hit->name(), "\n";
        while (my $hsp = $hit->next_hsp) {
            print "length is ", $hsp->length(), "\n";
        }
    }
}

🫶 okay so listen: do not use this class directly, it is available through Bio::SearchIO. That's the vibe, that's the rule.

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✨ DESCRIPTION ✨

This object implements a pull-parser for HMMER output 🧚 It's fast since it only does work on request (hence 'pull') — like, it's literally not gonna lift a finger until you ask it to, and honestly? iconic behaviour 💅

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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. 🥹

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. 🫶

🐛 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 _ 👀

🌟 new 🌟

Title   : new
Usage   : my $obj = Bio::SearchIO::hmmer_pull->new();
Function: Builds a new Bio::SearchIO::hmmer_pull object
Returns : Bio::SearchIO::hmmer_pull
Args    : -fh/-file => HMMER output filename
          -format   => 'hmmer_pull'
          -evalue   => float or scientific notation number to be used
                       as an evalue cutoff for hits
          -score    => integer or scientific notation number to be used
                       as a score value cutoff for hits
          -hsps     => integer minimum number of hsps (domains) a hit must have
          -piped_behaviour => 'temp_file'|'memory'|'sequential_read'

          -piped_behaviour defines what the parser should do if the input is
           an unseekable filehandle (eg. piped input), see
           Bio::PullParserI::chunk for details. Default is 'sequential_read'.

So like, you hand it a -fh/-file (that's your HMMER output filename, bestie), you tell it -format => 'hmmer_pull', and then there's the whole lil squad of cutoffs: -evalue (float or scientific notation number to be used as an evalue cutoff for hits), -score (integer or scientific notation number to be used as a score value cutoff for hits), and -hsps (integer minimum number of hsps (domains) a hit must have) 💅

And -piped_behaviour is 'temp_file'|'memory'|'sequential_read' — it defines what the parser should do if the input is an unseekable filehandle (eg. piped input), see Bio::PullParserI::chunk for details. Default is 'sequential_read'. 🫶

🦋 next_result 🦋

Title   : next_result
Usage   : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args    : none

⭐ result_count ⭐

Title   : result_count
Usage   : my $count = $searchio->result_count
Function: Returns the number of results we have processed.
Returns : integer
Args    : none

💜 rewind 💜

Title   : rewind
Usage   : $searchio->rewind;
Function: Allow one to reset the Result iterator to the beginning, so that
          next_result() will subsequently return the first result and so on.

          NB: result objects are not cached, so you will get new result objects
          each time you rewind. Also, note that result_count() counts the
          number of times you have called next_result(), so will not be able
          tell you how many results there were in the file if you use rewind().

Returns : n/a
Args    : none

🚨 okay bestie, read the fine print: result objects are not cached, so you will get new result objects each time you rewind. Also, note that result_count() counts the number of times you have called next_result(), so will not be able tell you how many results there were in the file if you use rewind(). fr fr, it's giving "the count is a lie" 💀

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and that's the whole page, babe 💖 this was perl v5.30.0, dated 2019-10-29, from the Bio::S...er_pull(3pm) era — mwah, slay, go parse some HMMER ✨