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Bio::SearchIO::megablast.3pm

NAME

Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports (format 0)

SYNOPSIS

# 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 ) {
       }
     }
   }
 
 

DESCRIPTION

Beware!

Because of the way megablast report format 0 is coded, realize that score means # gap characters + # mismatches for a HSP.

The docs from NCBI regarding FORMAT 0 # 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

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:

   http://bugzilla.open-bio.org/
 
 

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::blast->new();
  Function: Builds a new Bio::SearchIO::blast object
  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
  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:
  Example :
  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