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

💅 Bio::S...namotif — the manual, but make it cute 💅

okay so this is the User Contributed Perl Documentation page for Bio::S...namotif(3pm), and bestie, we're gonna walk through the whole thing together, no skips, no shortcuts. every flag, every arg, every vibe. let's go 🦋

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✨ NAME ✨

Bio::SearchIO::rnamotif — a SearchIO-based RNAMotif parser. that's the whole name section, short and iconic, we love a minimal queen 👑

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🌸 SYNOPSIS 🌸

  # do not call this module directly. Use Bio::SearchIO.

like literally, do NOT call this module directly, bestie. go through Bio::SearchIO. it's giving "use the front door, not the window" 🪟🙈

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💖 DESCRIPTION 💖

so. this is a highly experimental SearchIO-based parser for output from the rnamotif program — which is one of the programs in the RNAMotif suite, in case you were wondering 🧬

rn it parses only raw rnamotif output for RNAMotif versions 3.0 and above. older versions might work but will not be supported, so don't come for me. and rmfmt output? not supported at this time. periodt. 💀

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🫶 FEEDBACK 🫶

📬 Mailing Lists

user feedback is, like, an integral part of the evolution of this and other Bioperl modules. so 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

okay listen — direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. why? because many experienced and responsive experts will be able look at the problem and quickly address it 👑 (yes the original says "reponsive", we're keeping that typo, it's part of the lore now, no cap)

and pls pls pls include a thorough description of the problem with code and data examples if at all possible. the more context the better, bestie 🙏

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution together. 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

(shoutout to Chris, absolute legend for writing this 💜)

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that underscore is the "backstage pass, do not touch" indicator, iykyk 💅

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🌟 new

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

  -fh/-file     => RNAMotif filename
  -format       => 'rnamotif'
  -model        => query model (or descriptor, in this case)
  -database     => database name (default undef)
  -query_acc    => query accession (default undef)
  -hsp_minscore => minimum HSP score cutoff
  -hsp_maxscore => maximum HSP score cutoff
  -symbols      => hash ref of structure symbols to use
                   (default symbols in %STRUCTURE_SYMBOLS hash)

look at all those args, she's thriving ✨

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🌟 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

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🌟 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'

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🌟 end_element

• Title: start_element (yes that's what it says, we don't make the rules 🙈*)*
• Usage: $eventgenerator->end_element
• Function: Handles an end element event
• Returns: none
• Args: hashref with at least 2 keys, 'Data' and 'Name'

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🌟 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'

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🌟 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

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🌟 characters

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

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🌟 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

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🌟 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

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🌟 start_document

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

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🌟 end_document

• Title: end_document
• Usage: $eventgenerator->end_document
• Function: Handles an end document event
• Returns: Bio::Search::Result::ResultI object
• Args: none

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🌟 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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🌟 descriptor

• Title: descriptor
• Usage: my $descr = $parser->descriptor();
• Function: Get/Set descriptor name. Some versions of RNAMotif do not add the descriptor name to the output. This also overrides any name found while parsing.
• Returns: String (name of model)
• Args: [optional] String (name of model)

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🌟 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)
• Note: this is a synonym for descriptor()

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🌟 database

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

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🌟 query_accession

• Title: query_accession
• Usage: my $acc = $parser->query_accession();
• Function: Get/Set query (model) accession; RNAMotif currently does not output the accession number
• Returns: String (accession)
• Args: [optional] String (accession)

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🌟 algorithm_version

• Title: algorithm_version
• Usage: my $ver = $parser->algorithm_version();
• Function: Get/Set algorithm version (not defined in RNAMotif output)
• Returns: String (accession)
• Args: [optional] String (accession)

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🌟 hsp_minscore

• Title: hsp_minscore
• Usage: my $cutoff = $parser->hsp_minscore();
• Function: Get/Set min score cutoff (for generating Hits/HSPs).
• Returns: score (number)
• Args: [optional] score (number)
• Note: Cannot be set along with hsp_maxscore()

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🌟 hsp_maxscore

• Title: hsp_maxscore
• Usage: my $cutoff = $parser->hsp_maxscore();
• Function: Get/Set max score cutoff (for generating Hits/HSPs).
• Returns: score (number)
• Args: [optional] score (number)
• Note: Cannot be set along with hsp_minscore()

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🌟 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)

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

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🌟 _motif2meta

• Title: _motif2meta
• Usage: my ($rna, $meta) = $parser->_motif2meta($str, $descr);
• Function: Creates meta string from sequence and descriptor
• Returns: array of sequence, meta strings
• Args: Array of string data and descriptor data

Note: This is currently a quick and simple way of making simple RNA structures (stem-loops, helices, etc) from RNAMotif descriptor data in the output file. It does not currently work with pseudoknots, triplets, G-quartets, or other more complex RNA structural motifs.

like she said — quick and simple. don't try to feed her pseudoknots, she will simply not 💀

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and that's the whole page bestie!! 🎉 every method, every arg, every note, nothing skipped, we ate and left no crumbs 💅✨

this was perl v5.32.1, dated 2021-08-15, and the page itself is Bio::S...namotif(3pm) — go forth and parse responsibly 🦋🌸