Bio::S...:hmmer2(3pm)

✨ Bio::SearchIO::hmmer2 ✨

okay bestie, so this page is literally titled Bio::S...:hmmer2(3pm) — she's a User Contributed Perl Documentation girlie and she's here to make HMMER output make sense 💖

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🌸 NAME 🌸

Bio::SearchIO::hmmer2 — a parser for HMMER output (hmmpfam, hmmsearch). no cap, that's the whole job description 💅

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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 => 'hmmer2',
                            -file   => 't/data/L77119.hmmer');
while( my $result = $in->next_result ) {
    # this is a Bio::Search::Result::HMMERResult 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";
        }
    }
}

🚨 IMPORTANT GORL 🚨 do NOT use this class directly. she's available through Bio::SearchIO, that's the vibe. periodt.

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🌈 DESCRIPTION 🌈

This object implements a parser for HMMER output. that's it, that's the whole girl 🦋

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, she grows because of y'all 🫶. 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. like, no DMs please bestie 🙈. 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 — receipts, always receipts ✨

🐛 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 - Jason Stajich 👑

Email jason-at-bioperl.org — the icon who wrote her 💅✨

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, that underscore means she's private, don't touch her 🧚)

⭐ 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

⭐ start_element ⭐

• Title : start_element
• Usage : $eventgenerator->start_element
• Function: Handles a start element event
• Returns : none
• Args : hashref with at least 2 keys 'Data' and 'Name'

⭐ end_element ⭐

• Title : start_element
• Usage : $eventgenerator->end_element
• Function: Handles an end element event
• Returns : none
• Args : hashref with at least 2 keys 'Data' and 'Name'

👀 yes, the Title really says start_element on the end_element entry. we do not edit the ancestors, we just report the lore.

⭐ element ⭐

• Title : element
• Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
• Function: Convience method that calls start_element, characters, end_element
• Returns : none
• Args : Hash ref with the keys 'Name' and 'Data'

⭐ characters ⭐

• Title : characters
• Usage : $eventgenerator->characters($str)
• Function: Send a character events
• Returns : none
• Args : string

⭐ within_element ⭐

• Title : within_element
• Usage : if( $eventgenerator->within_element($element) ) {}
• Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block.
• Returns : boolean
• Args : string element name

⭐ in_element ⭐

• Title : in_element
• Usage : if( $eventgenerator->in_element($element) ) {}
• Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediete parent.
• Returns : boolean
• Args : string element name

⭐ start_document ⭐

• Title : start_document
• Usage : $eventgenerator->start_document
• Function: Handle a start document event
• Returns : none
• Args : none

⭐ end_document ⭐

• Title : end_document
• Usage : $eventgenerator->end_document
• Function: Handles an end document event
• 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

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and that's the whole page bestie 🫶 this version was served up by perl v5.30.0, dated 2019-10-29 — an absolute vintage, she's aging like fine wine 🍓 go parse some HMMER output and slay 💖✨