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)