Bio::SearchIO::fasta(3pm) | User Contributed Perl Documentation | Bio::SearchIO::fasta(3pm) |
Bio::SearchIO::fasta - A SearchIO parser for FASTA results
# Do not use this object directly, use it through the SearchIO system use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-format => 'fasta', -file => 'report.FASTA'); while( my $result = $searchio->next_result ) { # ... do what you would normally doi with Bio::SearchIO. }
This object contains the event based parsing code for FASTA format reports. It creates Bio::Search::HSP::FastaHSP objects instead of Bio::Search::HSP::GenericHSP for the HSP objects.
This module will parse -m 9 -d 0 output as well as default m 1 output from FASTA as well as SSEARCH.
Also see the SearchIO HOWTO: <http://bioperl.org/howtos/SearchIO_HOWTO.html>.
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.
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Please direct usage questions or support issues to the mailing list:
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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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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::fasta->new(); Function: Builds a new Bio::SearchIO::fasta object Returns : Bio::SearchIO::fasta Args : -idlength - set ID length to something other than the default (6), this is only necessary if you have compiled FASTA with a new default id length to display in the HSP alignment blocks
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 : 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 : idlength Usage : $obj->idlength($newval) Function: Internal storage of the length of the ID desc in the HSP alignment blocks. Defaults to $IDLENGTH class variable value Returns : value of idlength Args : newvalue (optional)
Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none
Title : _will_handle Usage : Private method. For internal use only. if( $self->_will_handle($type) ) { ... } Function: Provides an optimized way to check whether or not an element of a given type is to be handled. Returns : Reference to EventHandler object if the element type is to be handled. undef if the element type is not to be handled. Args : string containing type of element.
Optimizations:
This does not lead to a major savings by itself (only 5-10%). In combination with other optimizations, or for large parse jobs, the savings good be significant.
To test against the unoptimized version, remove the parentheses from around the third term in the ternary " ? : " operator and add two calls to $self->_eventHandler().
Title : _processHits Usage : Private method. For internal use only. Function: Process/report any hits/hsps we saw in the top table, not in alignments. Returns : nothing. Args : array of hits to process.
2020-10-28 | perl v5.30.3 |