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

✨ NAME ✨

Bio::SearchIO::erpin — it's a SearchIO-based parser for ERPIN, bestie 💅

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🌸 SYNOPSIS 🌸

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

okay so real talk: do NOT call this module directly, bestie 😭 use Bio::SearchIO. That's the whole vibe. Periodt.

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🦋 DESCRIPTION 🦋

So this is an experimental SearchIO-based parser that reads output from the erpin program ✨

Right now it parses erpin output for ERPIN versions 4.2.5 and above. Older versions? They might work, but like... nobody's supporting that, ngl. 🙈

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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 so 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 🙏 That way many experienced and responsive experts can look at the problem and quickly address it. And please include a thorough description of the problem, with code and data examples if at all possible. Give us the whole story, not just the vibes 💅

🐛 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 - Chris Fields 👑

Email cjfields-at-uiuc-dot-edu

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods 🧚 Internal methods are usually preceded with a _ (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 => 'erpin'
  • -algorithm => algorithm (default 'Infernal')
  • -query_acc => query accession, eg. Rfam accession (default undef)
  • -hsp_minscore => minimum HSP score cutoff
  • -version => ERPIN version (not reported in output)

🍓 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 bestie, the Title on this one literally says start_element in the original too. We don't fix, we report. 💀

💜 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

💅 query_accession

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

🍓 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)

👑 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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and that's the whole page, bestie 🫶 this one's Bio::SearchIO::erpin from the User Contributed Perl Documentation, running on perl v5.32.1, dated 2021-08-15 ✨ go forth and parse responsibly 💜