Bio::S...:hmmer3(3pm)

💖 NAME 💖

Bio::SearchIO::hmmer3 — it's the module in the Bioperl family that reads HMMER output and hands it to you as nice tidy objects. This page lives in the User Contributed Perl Documentation (the 3pm crew, you know the vibe ✨).

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🦋 SYNOPSIS 🦋

use Bio::SearchIO;

my $searchio = Bio::SearchIO->new(
    -format  => 'hmmer',
    -version => 3,
    -file    => 'hmmsearch.out' );

my $result = $searchio->next_result; my $hit = $result->next_hit; print
$hit->name, $hit->description, $hit->significance,
      $hit->score, "\n";

my $hsp = $hit->next_hsp; print $hsp->start('hit'), $hsp->end('hit'),
$hsp->start('query'),
      $hsp->end('query'), "\n";

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🌸 DESCRIPTION 🌸

Okay so bestie, this is the code that parses output from hmmsearch, hmmscan, phmmer and nhmmer — and it's compatible with both version 2 and version 3 of the HMMER package from <http://hmmer.org>. Both versions. It said what it said 💅

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is literally 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, 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. There are so many experienced and responsive experts who'll be able look at the problem and quickly address it. If at all possible, please include a thorough description of the problem with code and data examples. Give them the full picture, they deserve it 🙈

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can 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 - Thomas Sharpton 👑

Email thomas.sharpton@gmail.com

Describe contact details here

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🌈 CONTRIBUTORS 🌈

Additional contributors names and emails here

briano at bioteam.net

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⭐ APPENDIX ⭐

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, the underscore ones are the behind-the-scenes girlies).

✨ 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 event
Returns : none
Args    : hashref with at least 2 keys 'Data' and 'Name'

✨ end_element

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

✨ element

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

✨ get_from_element

Title   : get_from_element
Usage   : $self->get_from_element('HSP-hit_start');
Function: Convenience method to retrieve data from '_values' hash
Returns : string
Args    : key

✨ 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 immediate 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 processed
Returns : integer
Args    : none

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okay that's the whole page, you ate it up 💖 this one's perl v5.30.0, dated 2019-10-29, and it's the Bio::SearchIO::hmmer3(3pm) page from the User Contributed Perl Documentation. periodt. 🎀✨