Bio::SearchIO::blastxml man page on Pidora

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Bio::SearchIO::blastxmUser Contributed Perl DocumentBio::SearchIO::blastxml(3)

NAME
       Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML
       parsing.

SYNOPSIS
	   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 ) {
	   }

DESCRIPTION
       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).

DEPENDENCIES
       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/

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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       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.

   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:

	 http://bugzilla.open-bio.org/

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 $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.

   _initialize
	Title	: _initialize
	Usage	: private
	Function: Initializes the object - this is chained through new in SearchIO

   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

   result_count
	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

   use_tempfile
	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)

   blasttype
	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)

perl v5.14.1			  2011-07-22	    Bio::SearchIO::blastxml(3)
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