Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
use Bio::SearchIO; my $searchin = Bio::SearchIO->new(-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 = Bio::SearchIO->new(-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. It requires XML::SAX; it is also recommended (for faster parsing) that XML::SAX::ExpatXS or XML::LibXML be installed. Either 'XML::SAX::ExpatXS' or 'XML::LibXML::SAX::Parser' should be set as the default parser in ParserDetails.ini. This file is located in the SAX subdirectory of XML in your local perl library (normally in the 'site' directory).
Currently, XML::SAX::Expat will not work and will not be supported.
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).
In addition to parts of the Bio:: hierarchy, this module uses:
XML::SAX
It is also recommended that XML::SAX::ExpatXS be installed and made the default XML::SAX parser using , along with the Expat library () for faster parsing. XML::SAX::Expat is not recommended; XML::SAX::ExpatXS is considered the current replacement for XML::SAX:Expat and is actively being considered to replace XML::SAX::Expat. XML::SAX::Expat will work, but only if you have local copies of the NCBI BLAST DTDs. This is due to issues with NCBI's BLAST XML format. The DTDs and the web address to obtain them are:
NCBI_BlastOutput.dtd NCBI_BlastOutput.mod.dtd http://www.ncbi.nlm.nih.gov/data_specs/dtd/
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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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/
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 $searchio = Bio::SearchIO->new(-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 : result_count Usage : $num = $stream->result_count; Function: Gets the number of Blast results that have been successfully parsed at the point of the method call. This is not the total # of results in the file. Returns : integer Args : none Throws : none
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)
Title : blasttype Usage : $obj->blasttype($newtype) Function: Get/Set BLAST report type. Returns : BLAST report type Args : case-insensitive string of types BLAST or PSIBLAST (default: BLAST) Note : this is used to determine how reports are 'chunked' (in cases where multiple queries are submitted) and which XML handler to use when parsing the report(s)
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.