Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
use Bio::SearchIO; my $searchin = new Bio::SearchIO(-format => 'blastxml', -file => 't/data/plague_yeast.bls.xml'); while( my $result = $searchin->next_result ) { } # one can also request that the parser NOT keep the XML data in memory # by using the tempfile initialization flag. my $searchin = new Bio::SearchIO(-tempfile => 1, -format => 'blastxml', -file => 't/data/plague_yeast.bls.xml'); while( my $result = $searchin->next_result ) { }
This object implements a NCBI Blast XML parser.
There is one additional initialization flag from the SearchIO defaults - that is the -tempfile flag. If specified as true, then the parser will write out each report to a temporary filehandle rather than holding the entire report as a string in memory. The reason this is done in the first place is NCBI reports have an uncessary <?xml version="1.0"?> at the beginning of each report and RPS-BLAST reports have an additional unecessary RPS-BLAST tag at the top of each report. So we currently have implemented the work around by preparsing the file (yes it makes the process slower, but it works).
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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 $searchio = new Bio::SearchIO(-format => 'blastxml', -file => 'filename', -tempfile => 1); Function: Initializes the object - this is chained through new in SearchIO Returns : Bio::SearchIO::blastxml object Args : One additional argument from the format and file/fh parameters. -tempfile => boolean. Defaults to false. Write out XML data to a temporary filehandle to send to PerlSAX parser.
Title : _initialize Usage : private Function: Initializes the object - this is chained through new in SearchIO
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_document Usage : $parser->start_document; Function: SAX method to indicate starting to parse a new document Returns : none Args : none
Title : end_document Usage : $parser->end_document; Function: SAX method to indicate finishing parsing a new document Returns : Bio::Search::Result::ResultI object Args : none
Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data
Title : end_element Usage : $parser->end_element($data) Function: Signals finishing an element Returns : Bio::Search object dpending on what type of element Args : hash ref for data
Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data'
Title : use_tempfile Usage : $obj->use_tempfile($newval) Function: Get/Set boolean flag on whether or not use a tempfile Example : Returns : value of use_tempfile Args : newvalue (optional)
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.