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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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::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