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

✨ NAME ✨

okay so bestie, this page is Bio::S...ablast(3pm), from the User Contributed Perl Documentation, and it's literally all about Bio::SearchIO::megablast — a driver module for Bio::SearchIO that parses megablast reports (format 0). no cap. 💅

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🎀 SYNOPSIS 🎀

⚠️ do not use this module directly — fr fr, hands off, it's giving backstage pass only 🙈

# do not use this module directly

  use Bio::SearchIO;
  # for default format output from megablast
  my $in = Bio::SearchIO->new(-file   => 'file.mbl',
                             -format => 'megablast',
                             -report_format => 0);

  while( my $r = $in->next_result ) {
    while( my $hit = $r->next_hit ) {
      while( my $hsp = $hit->next_hsp ) {
      }
    }
  }

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😭 DESCRIPTION 😭

Beware! like, genuinely, heads up bestie. 🫶

Because of the way megablast report format 0 is coded, realize that score means # gap characters + # mismatches for a HSP. that's the whole vibe, no cap.

The docs from NCBI regarding FORMAT 0, and I'm quoting here so you get it exactly:

#   0: Produce one-line output for each alignment, in the form
# #   'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score
# #   Here subject(query)-id is a gi number, an accession or some other type of
#   identifier found in the FASTA definition line of the respective sequence.
# #
#   + or - corresponds to same or different strand alignment.
# #
#   Score for non-affine gapping parameters means the total number of
#   differences (mismatches + gap characters). For affine case it is the
#   actual (raw) score of the alignment.

FORMAT 1 parsing has not been implemented 😭 FORMAT 2 parsing should work with the SearchIO 'blast' parser. 🌈

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💌 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

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👑 AUTHOR - Jason Stajich 👑

Email jason-at-bioperl.org ✨

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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::blast->new();
• Function: Builds a new Bio::SearchIO::blast object — brand new, fresh out the box 🎁
• Returns: Bio::SearchIO::blast
• Args:
  • -fh/-file => filehandle/filename to BLAST file
  • -format => 'blast'

💜 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

💜 report_format

• Title: report_format
• Usage: $obj->report_format($newval)
• Function: Get/Set the report_format value
• Returns: value of report_format (a scalar)
• Args: on set, new value (a scalar or undef, optional)

💜 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 (yes, the title says start_element in the original — iconic little glitch, keeping 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

💜 _mode

• Title: _mode
• Usage: $obj->_mode($newval)
• Function: (blank in the original, bestie — not a single word, and I'm not about to invent one) 🙈
• Example: (also blank)
• Returns: value of _mode
• Args: newvalue (optional)

💜 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: Handles 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

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and that's the whole page bestie, we ate and left no crumbs 🍽️✨ this one's from perl v5.32.1, dated 2021-08-15, and the page name is Bio::S...ablast(3pm). mwah, go parse some megablast reports 💖🦋🌸