Bio::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.

    $searchin = Bio::SearchIO->new(-tempfile => 1,
                                     -format => 'blastxml',
                                     -file   => 't/data/plague_yeast.bls.xml');

    while( my $result = $searchin->next_result ) {
       ....
    }

    # PSI-BLAST parsing (default is normal BLAST)
    $searchin = Bio::SearchIO->new(
                     -format => 'blastxml',
                     -blasttype => 'psiblast',
                                     -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).

Two different XML handlers currently exist to deal with logical differences between how normal BLAST reports and PSI-BLAST reports are logically parsed into BioPerl objects; this is explicitly settable using the -blasttype parameter. The default is for parsing a normal BLAST report ('blast'), but if one is expecting PSI-BLAST report parsing, -blasttype must be set explicitly to 'psiblast'. This is due to a lack of any information in the XML output which tells the parser the report is derived from a PSI-BLAST run vs. a normal BLAST run.

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 unnecessary 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). We are open to suggestions on how to optimize this in the future.

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:

  https://github.com/bioperl/bioperl-live/issues

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)