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

💖 Bio::SearchIO::cross_match — the manual, but make it cute 💖

perl v5.32.1 · User Contributed Perl Documentation · bestie edition 🫶

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✨ NAME ✨

Bio::SearchIO::cross_match — it's the CrossMatch-specific subclass of Bio::SearchIO, and yes she's giving "specialized baby of a bigger module" and we love her for it 💅

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🦋 SYNOPSIS 🦋

okay so here's the vibe — you're working with iterations (CrossMatch results), and it goes a lil something like this:

# Working with iterations (CrossMatch results)
my $searchIO = Bio::SearchIO->new( -format => 'cross_match',
                        -file   => "$file.screen.out" )
while(my $r = $searchIO->next_result) {
  while(my $hit = $r->next_hit) {
          while(my $hsp = $hit->next_hsp) {
       #Do the processing here.
    }
  }
}

And fr fr, if you wanna know the whole lore about working with Bio::SearchIO, go peek at Bio::SearchIO — it's all there, no cap 📖✨

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🌸 DESCRIPTION 🌸

So basically: this object is a subclass of Bio::SearchIO, and she serves up some operations that make working with CrossMatch (and CrossMatch results) actually doable 💖

For the general tea on working with Results, you're gonna wanna check out Bio::Search::Result::GenericResult — she's the main character for that 🎀

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is literally an integral part of the evolution of this module and all the other Bioperl modules — so pls, send your comments and suggestions, preferably to the Bioperl mailing list. Your participation is so appreciated, genuinely 🥹🫶

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

🛟 Support

Bestie, direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

— and not straight to the module maintainer, ok? There are so many experienced and responsive experts on the list who can look at your problem and address it quickly. If you can, pls include a thorough description of the problem with code and data examples. That's the slay way to ask 💅✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — it's a whole system, respect it 🙌 Bug reports can be submitted via the web:

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

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👑 AUTHOR - Shin Leong 👑

Email: sleong@watson.wustl.edu

(iconic, we stan 💜)

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🌈 CONTRIBUTORS 🌈

Additional contributors names and emails here

(yes, that's literally what it says, the list is a placeholder and I am simply passing the message along, no notes 🙈)

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📚 APPENDIX 📚

The rest of the documentation details each of the object methods. Heads up: internal methods are usually preceded with a _ — that underscore is basically their "do not perceive me" marker 🫣

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🔁 next_result

• Title: next_result
• Usage: $result = stream->next_result
• Function: Reads the next ResultI object from the stream and returns it.

Okay so here's the important part, listen up: certain driver modules may encounter entries in the stream that are either misformatted or that use syntax not yet understood by the driver. If such an incident is recoverable — like, say, by dismissing a feature of a feature table or some other non-mandatory part of an entry — the driver will issue a warning. But in the case of a non-recoverable situation, an exception will be thrown 😭

Do not assume that you can resume parsing the same stream after catching the exception. That is not a thing. It's not giving "try again bestie", it's giving "this stream is done".

Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2) (see the Bio::Root::RootI POD page) — your choice, your power ✨

• Returns: A Bio::Search::Result::ResultI object
• Args: n/a

See Bio::Root::RootI

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🔒 _alignment

• Title: _alignment
• Usage: private

(that's it, that's the whole entry, she's private and mysterious 🫣💅)

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🔒 _parse

• Title: _parse
• Usage: private

(also private, also mysterious, also not telling us anything, respect the privacy 🎀)

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🔢 result_count

• Title: result_count
• Usage: $num = $stream->result_count;
• Function: Gets the number of CrossMatch results that have been parsed.
• Returns: integer
• Args: none
• Throws: none

literally just a counter, she counts, she returns, no drama, no throwing, immaculate behaviour 👑

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🫶 cute sign-off 🫶

This lil page came to you from perl v5.32.1, dated 2021-08-15, filed under Bio::S..._match(3pm) — yeah the title's a lil abbreviated, she's got main character energy with a short name, and honestly? iconic. Go parse something, bestie 💖✨🌸🦋