| Bio::SearchIO::megablast(3pm) | User Contributed Perl Documentation | Bio::SearchIO::megablast(3pm) |
Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports (format 0)
# 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 ) {
}
}
}
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
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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.
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:
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Email jason-at-bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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'
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
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)
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'
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'
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'
Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string
Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional)
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
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
Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none
Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none
Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none
| 2020-10-28 | perl v5.30.3 |