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

💖 NAME 💖

Bio::SearchIO::exonerate — no cap, it's the parser for Exonerate 💅

---

✨ SYNOPSIS ✨

okay so listen: do not use this module directly, it is a driver for SearchIO. like, that's the whole vibe, bestie.

# do not use this module directly, it is a driver for SearchIO

use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-file => 'file.exonerate',
                                 -format => 'exonerate');

while( my $r = $searchio->next_result ) {
  print $r->query_name, "\n";
}

---

🦋 DESCRIPTION 🦋

So this is a driver for the SearchIO system for parsing Exonerate (Guy Slater) output. You can get Exonerate at http://www.ebi.ac.uk/~guy/exonerate/ [until Guy puts up a Web reference,publication for it.]). 🫶

An optional parameter -min_intron is supported by the new initialization method. This is if you run Exonerate with a different minimum intron length (default is 30) the parser will be able to detect the difference between standard deletions and an intron. Still some room to play with there that might cause this to get misinterpreted that has not been fully tested or explored. 🙈

The VULGAR and CIGAR formats should be parsed okay now creating HSPs where appropriate (so merging match states where appropriate rather than breaking an HSP at each indel as it may have done in the past). The GFF that comes from exonerate is still probably a better way to go if you are doing protein2genome or est2genome mapping. For example you can see this script:

### TODO: Jason, this link is dead, do we have an updated one?
http://fungal.genome.duke.edu/~jes12/software/scripts/process_exonerate_gff3.perl.txt

👀 bestie that TODO is literally in the original, I'm not making it up, the link is dead and the comment says so.

If your report contains both CIGAR and VULGAR lines only the first one will processed for a given Query/Target pair. If you preferentially want to use VULGAR or CIGAR add one of these options when initializing the SearchIO object.

-cigar  => 1

OR

-vulgar => 1

Or set them via these methods.

$parser->cigar(1)

OR

$parser->vulgar(1)

---

🌸 FEEDBACK 🌸

💌 Mailing Lists

User feedback is 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. 🥹

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. 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. 🙏

🐛 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

---

👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl.org ✨

---

🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 🧚

🌟 new

• Title: new
• Usage: my $obj = Bio::SearchIO::exonerate->new();
• Function: Builds a new Bio::SearchIO::exonerate object
• Returns: an instance of Bio::SearchIO::exonerate
• Args:
  • -min_intron => somewhat obsolete option, how to determine if a an indel is an intron or a local gap. Use VULGAR rather than CIGAR to avoid this heuristic,default 30.
  • -cigar => 1 — set this to 1 if you want to parse CIGAR exclusively.
  • -vulgar => 1 — set this to 1 if you want to parse VULGAR exclusively, setting both to 1 will revert to the default behavior of just parsing the first line that it sees.

🌟 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 (yeah bestie, that's what the original says, I'm not touching it 💀)
• 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: 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 'in' because within can be tested for a whole block.
• 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

🌟 vulgar

• Title: vulgar
• Usage: $obj->vulgar($newval)
• Function: Get/Set flag, do you want to build HSPs from VULGAR string?
• Returns: value of vulgar (a scalar)
• Args: on set, new value (a scalar or undef, optional)

🌟 cigar

• Title: cigar
• Usage: $obj->cigar($newval)
• Function: Get/Set boolean flag do you want to build HSPs from CIGAR strings?
• Returns: value of cigar (a scalar)
• Args: on set, new value (a scalar or undef, optional)

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and that's the whole page bestie, you ate 💅✨

this one's from User Contributed Perl Documentation, version perl v5.32.1, dated 2021-08-15, and the page itself is Bio::S...nerate(3pm) — go forth and parse some Exonerate output, ily 🫶🎀🦋