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

💖 NAME 💖

okay bestie, welcome to the Bio::S...nfernal(3pm) page — that's the manual name right there, sitting in the User Contributed Perl Documentation collection. What it actually is: Bio::SearchIO::infernal, a SearchIO-based Infernal parser. 💅

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✨ SYNOPSIS ✨

  my $parser = Bio::SearchIO->new(-format => 'infernal',
                                  -file => 'purine.inf');
  while( my $result = $parser->next_result ) {
        # general result info, such as model used, Infernal version
        while( my $hit = $result->next_hit ) {
            while( my $hsp = $hit->next_hsp ) {
                # ...
            }
        }
  }

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🌸 DESCRIPTION 🌸

So this is a SearchIO-based parser that eats Infernal output from the cmsearch program. 🦋 Right now it parses cmsearch output for Infernal versions 0.7–1.1. Older versions might technically work, but like… nobody's supporting them, and that's the tea. 💀

The latest Infernal version is 1.1. The output changed a lot compared to version 1.0. Versions 1.x are stable releases (and the output has stabilized too), so it's highly recommended that you upgrade to the newest Infernal release. Support for those older pre-v.1 developer releases? Getting dropped for future core 1.6 releases. Sorry not sorry, it's giving deprecated. 🫶

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🫶 FEEDBACK 🫶

💌 Mailing Lists

User feedback is a whole integral part of how this and other Bioperl modules evolve, bestie. Send your comments and suggestions (preferably) to the Bioperl mailing list. Your participation is so appreciated. 🥹

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🩹 Support

Please send usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

…rather than sliding into the module maintainer's DMs directly. There are so many experienced and responsive experts there who can look at your problem and fix it fast. If at all possible, include a thorough description of the problem with code and data examples. Give them the whole picture, no crumbs. ✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so everyone can keep track of them and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR - Chris Fields 👑

Email: cjfields-at-uiuc-dot-edu

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🌈 CONTRIBUTORS 🌈

  Jeffrey Barrick, Michigan State University
  Paul Cantalupo, University of Pittsburgh

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🎀 APPENDIX 🎀

The rest of this documentation spills the details on each of the object methods. Internal methods are usually prefixed with an _. iykyk. 🔥

🧚 new

• Title: new
• Usage: my $obj = Bio::SearchIO::infernal->new();
• Function: Builds a new Bio::SearchIO::infernal object
• Returns: Bio::SearchIO::infernal
• Args:

-fh/-file      => cmsearch (infernal) filename
-format        => 'infernal'
-model         => query model (Rfam ID) (default undef)
-database      => database name (default undef)
-query_acc     => query accession, eg. Rfam accession RF####
-query_desc    => query description, eg. Rfam description
-hsp_minscore  => minimum HSP score cutoff
-convert_meta  => boolean, set to convert meta string to simple WUSS format
-symbols       => hash ref of structure symbols to use
                  (default symbols in %STRUCTURE_SYMBOLS hash)

🦋 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'

💜 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'

💜 element_hash

• Title: element
• Usage:

  $eventhandler->element_hash({'Hsp_hit-from' => $start,
                               'Hsp_hit-to'   => $end,
                               'Hsp_score'    => $lastscore});

• Function: Convenience method that takes multiple simple data elements and maps to appropriate parameters
• Returns: none
• Args: Hash ref with the mapped key (in %MAPPING) and value

🍓 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 we have processed
• Returns: integer
• Args: none

🧬 model

• Title: model
• Usage: my $model = $parser->model();
• Function: Get/Set model; Infernal currently does not output the model name (Rfam ID)
• Returns: String (name of model)
• Args: [optional] String (name of model)

🗄️ database

• Title: database
• Usage: my $database = $parser->database();
• Function: Get/Set database; pre-v.1 versions of Infernal do not output the database name
• Returns: String (database name)
• Args: [optional] String (database name)

⚙️ algorithm

• Title: algorithm
• Usage: my $algorithm = $parser->algorithm();
• Function: Get/Set algorithm; pre-v.1 versions of Infernal do not output the algorithm name
• Returns: String (algorithm name)
• Args: [optional] String (algorithm name)

🔑 query_accession

• Title: query_accession
• Usage: my $acc = $parser->query_accession();
• Function: Get/Set query (model) accession; pre-v1.1 Infernal does not output the accession number (Rfam accession #)
• Returns: String (accession)
• Args: [optional] String (accession)

📝 query_description

• Title: query_description
• Usage: my $acc = $parser->query_description();
• Function: Get/Set query (model) description; pre-v1.1 Infernal does not output the Rfam description
• Returns: String (description)
• Args: [optional] String (description)

✂️ hsp_minscore

• Title: hsp_minscore
• Usage: my $cutoff = $parser->hsp_minscore();
• Function: Get/Set min bit score cutoff (for generating Hits/HSPs)
• Returns: score (number)
• Args: [optional] score (number)

🔄 convert_meta

• Title: convert_meta
• Usage: $parser->convert_meta(1);
• Function: Get/Set boolean flag for converting Infernal WUSS format to a simple bracketed format (simple WUSS by default)
• Returns: boolean flag (TRUE or FALSE)
• Args: [optional] boolean (eval's to TRUE or FALSE)

🏷️ version

• Title: version
• Usage: $parser->version();
• Function: Set the Infernal cmsearch version
• Returns: version
• Args: [optional] version

🪢 structure_symbols

• Title: structure_symbols
• Usage: my $hashref = $parser->structure_symbols();
• Function: Get/Set RNA structure symbols
• Returns: Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)

default = < (5-prime)
          > (3-prime)
          : (single-strand)
          ? (unknown)
          . (gap)

• Args: Hash ref of substitute delimiters, using above keys.

🌸 simple_meta

• Title: simple_meta
• Usage: my $string = $parser->simple_meta($str);
• Function: converts more complex WUSS meta format into simple bracket format using symbols defined in structure_symbols()
• Returns: converted string
• Args: [required] string to convert
• Note: This is a very simple conversion method to get simple bracketed format from Infernal data. If the convert_meta() flag is set, this is the method used to convert the strings.

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and that's the whole page, bestie, you ate it up 💅 — this was Bio::S...nfernal(3pm), generated for perl v5.32.1 on 2021-08-15. go forth and parse, main character. 🎀✨🦋