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BLAST XML not allowing custom search handlers, fix that
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Chris Fields committed Nov 4, 2012
1 parent 0d6cf26 commit 6fe0323
Showing 1 changed file with 55 additions and 37 deletions.
92 changes: 55 additions & 37 deletions Bio/SearchIO/blastxml.pm
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Original file line number Original file line Diff line number Diff line change
@@ -1,7 +1,7 @@
# #
# BioPerl module for Bio::SearchIO::blastxml # BioPerl module for Bio::SearchIO::blastxml
# #
# Please direct questions and support issues to <bioperl-l@bioperl.org> # Please direct questions and support issues to <bioperl-l@bioperl.org>
# #
# Cared for by Jason Stajich <jason@bioperl.org> # Cared for by Jason Stajich <jason@bioperl.org>
# #
Expand All @@ -13,35 +13,35 @@


=head1 NAME =head1 NAME
Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing. Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
=head1 SYNOPSIS =head1 SYNOPSIS
use Bio::SearchIO; use Bio::SearchIO;
my $searchin = Bio::SearchIO->new(-format => 'blastxml', my $searchin = Bio::SearchIO->new(-format => 'blastxml',
-file => 't/data/plague_yeast.bls.xml'); -file => 't/data/plague_yeast.bls.xml');
while( my $result = $searchin->next_result ) { while( my $result = $searchin->next_result ) {
.... ....
} }
# one can also request that the parser NOT keep the XML data in memory # one can also request that the parser NOT keep the XML data in memory
# by using the tempfile initialization flag. # by using the tempfile initialization flag.
$searchin = Bio::SearchIO->new(-tempfile => 1, $searchin = Bio::SearchIO->new(-tempfile => 1,
-format => 'blastxml', -format => 'blastxml',
-file => 't/data/plague_yeast.bls.xml'); -file => 't/data/plague_yeast.bls.xml');
while( my $result = $searchin->next_result ) { while( my $result = $searchin->next_result ) {
.... ....
} }
# PSI-BLAST parsing (default is normal BLAST) # PSI-BLAST parsing (default is normal BLAST)
$searchin = Bio::SearchIO->new( $searchin = Bio::SearchIO->new(
-format => 'blastxml', -format => 'blastxml',
-blasttype => 'psiblast', -blasttype => 'psiblast',
-file => 't/data/plague_yeast.bls.xml'); -file => 't/data/plague_yeast.bls.xml');
while( my $result = $searchin->next_result ) { while( my $result = $searchin->next_result ) {
.... ....
} }
Expand Down Expand Up @@ -88,7 +88,7 @@ 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 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: DTDs and the web address to obtain them are:
NCBI_BlastOutput.dtd NCBI_BlastOutput.dtd
NCBI_BlastOutput.mod.dtd NCBI_BlastOutput.mod.dtd
http://www.ncbi.nlm.nih.gov/data_specs/dtd/ http://www.ncbi.nlm.nih.gov/data_specs/dtd/
Expand All @@ -104,15 +104,15 @@ the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support =head2 Support
Please direct usage questions or support issues to the mailing list: Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org> I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem address it. Please include a thorough description of the problem
with code and data examples if at all possible. with code and data examples if at all possible.
=head2 Reporting Bugs =head2 Reporting Bugs
Expand Down Expand Up @@ -180,7 +180,7 @@ my %VALID_TYPE = (
=cut =cut


sub _initialize{ sub _initialize{
my ($self,@args) = @_; my ($self,@args) = @_;
$self->SUPER::_initialize(@args); $self->SUPER::_initialize(@args);
my ($usetempfile, $blasttype,$xmlcompact) = $self->_rearrange([qw( my ($usetempfile, $blasttype,$xmlcompact) = $self->_rearrange([qw(
TEMPFILE TEMPFILE
Expand All @@ -191,11 +191,29 @@ sub _initialize{
$self->blasttype(uc $blasttype); $self->blasttype(uc $blasttype);
defined $usetempfile && $self->use_tempfile($usetempfile); defined $usetempfile && $self->use_tempfile($usetempfile);
$self->{_result_count} = 0; $self->{_result_count} = 0;
eval { require Time::HiRes }; eval { require Time::HiRes };
if( $@ ) { $DEBUG = 0; } if( $@ ) { $DEBUG = 0; }
$DEBUG = 1 if( ! defined $DEBUG && ($self->verbose > 0)); $DEBUG = 1 if( ! defined $DEBUG && ($self->verbose > 0));
} }


sub attach_EventHandler {
my ($self,$handler) = @_;

$self->SUPER::attach_EventHandler($handler);

# Make sure if there is an XML parser present already, the internal Handler
# is set
if (exists $self->{'_xmlparser'}) {
$self->{'_xmlparser'}->get_handler->eventHandler($handler);
}

# Optimization: caching the EventHandler since it is used a lot
# during the parse.

$self->{'_handler_cache'} = $handler;
return;
}

=head2 next_result =head2 next_result
Title : next_result Title : next_result
Expand All @@ -208,14 +226,14 @@ sub _initialize{


sub next_result { sub next_result {
my ($self) = @_; my ($self) = @_;

my $result; my $result;


my ($tfh); my ($tfh);

# XMLCOMPACT # XMLCOMPACT
# WU-BLAST has an XML_COMPACT option which needs to be preprocessed before # WU-BLAST has an XML_COMPACT option which needs to be preprocessed before
# passing on to the parser. # passing on to the parser.
if ($self->{_xml_compact}) { if ($self->{_xml_compact}) {
$self->debug("XMLCOMPACT mode\n"); $self->debug("XMLCOMPACT mode\n");
my ($tfh2, $filename) = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!"); my ($tfh2, $filename) = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
Expand All @@ -230,17 +248,17 @@ sub next_result {
# redirect self's IO to use new tempfile # redirect self's IO to use new tempfile
$self->_fh($tfh2); $self->_fh($tfh2);
} }

if( $self->use_tempfile ) { if( $self->use_tempfile ) {
$tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!"); $tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
$tfh->autoflush(1); $tfh->autoflush(1);
} }

my $okaytoprocess = ($self->blasttype =~ /PSI/) ? $self->_chunk_psiblast($tfh) : my $okaytoprocess = ($self->blasttype =~ /PSI/) ? $self->_chunk_psiblast($tfh) :
$self->_chunk_normalblast($tfh); $self->_chunk_normalblast($tfh);

return unless( $okaytoprocess); return unless( $okaytoprocess);

my %parser_args; my %parser_args;
if( defined $tfh ) { if( defined $tfh ) {
seek($tfh,0,0); seek($tfh,0,0);
Expand All @@ -251,20 +269,20 @@ sub next_result {


my $starttime; my $starttime;
if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; } if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; }

eval { eval {
$result = $self->{'_xmlparser'}->parse(%parser_args); $result = $self->{'_xmlparser'}->parse(%parser_args);
}; };

if( $@ ) { if( $@ ) {
$self->warn("error in parsing a report:\n $@"); $self->warn("error in parsing a report:\n $@");
$result = undef; $result = undef;
} }
if( $DEBUG ) { if( $DEBUG ) {
$self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime))); $self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime)));
} }
# parsing magic here - but we call event handlers rather than # parsing magic here - but we call event handlers rather than
# instantiating things # instantiating things
if (defined $result) { if (defined $result) {
# result count is handled here, as the BLASTXML reports are # result count is handled here, as the BLASTXML reports are
# broken up into smaller easier to digest bits # broken up into smaller easier to digest bits
Expand Down Expand Up @@ -298,7 +316,7 @@ sub result_count {
Title : use_tempfile Title : use_tempfile
Usage : $obj->use_tempfile($newval) Usage : $obj->use_tempfile($newval)
Function: Get/Set boolean flag on whether or not use a tempfile Function: Get/Set boolean flag on whether or not use a tempfile
Example : Example :
Returns : value of use_tempfile Returns : value of use_tempfile
Args : newvalue (optional) Args : newvalue (optional)
Expand Down Expand Up @@ -337,13 +355,13 @@ sub blasttype{
print STDERR <<END; print STDERR <<END;
$self: data module $VALID_TYPE{$value} cannot be found $self: data module $VALID_TYPE{$value} cannot be found
Exception $@ Exception $@
For more information about the Bio::SearchIO::blastxml system please see the Bio::SearchIO::blastxml. For more information about the Bio::SearchIO::blastxml system please see the Bio::SearchIO::blastxml.
END END
return unless $ok; return unless $ok;
} }
# BlastHandler does the heavy lifting # BlastHandler does the heavy lifting
my $xmlhandler = $VALID_TYPE{$value}->new(-verbose => $self->verbose); my $xmlhandler = $VALID_TYPE{$value}->new(-verbose => $self->verbose);

# The XML handler does the heavy work, passes data to object handler # The XML handler does the heavy work, passes data to object handler
if ($value =~ /^PSI/) { if ($value =~ /^PSI/) {
my $handler = Bio::SearchIO::IteratedSearchResultEventBuilder->new(); my $handler = Bio::SearchIO::IteratedSearchResultEventBuilder->new();
Expand All @@ -356,7 +374,7 @@ END
Handler => $xmlhandler); Handler => $xmlhandler);
$self->{'_xmlparser'} = $parserfactory; $self->{'_xmlparser'} = $parserfactory;
$self->saxparser(ref($parserfactory)); $self->saxparser(ref($parserfactory));

$self->{'_blasttype'} = $value; $self->{'_blasttype'} = $value;
} }
return $self->{'_blasttype'}; return $self->{'_blasttype'};
Expand All @@ -369,13 +387,13 @@ sub saxparser {


sub _chunk_normalblast { sub _chunk_normalblast {
my ($self, $tfh) = @_; my ($self, $tfh) = @_;

local $/ = "\n"; local $/ = "\n";
local $_; local $_;
$self->{'_blastdata'} = ''; $self->{'_blastdata'} = '';

my ($sawxmlheader, $okaytoprocess); my ($sawxmlheader, $okaytoprocess);

my $mode = 'header'; my $mode = 'header';


my $tail = << 'XML_END'; my $tail = << 'XML_END';
Expand All @@ -385,7 +403,7 @@ XML_END


# no buffering needed (famous last words...) # no buffering needed (famous last words...)
my $fh = $self->_fh; my $fh = $self->_fh;

#chop up XML into edible bits for the parser #chop up XML into edible bits for the parser
while( defined( my $line = <$fh>) ) { while( defined( my $line = <$fh>) ) {
next if $line =~ m{^\s*</BlastOutput_iterations>}xmso || $line =~ m{^</BlastOutput>}xmso; next if $line =~ m{^\s*</BlastOutput_iterations>}xmso || $line =~ m{^</BlastOutput>}xmso;
Expand Down Expand Up @@ -426,16 +444,16 @@ XML_END


sub _chunk_psiblast { sub _chunk_psiblast {
my ($self, $tfh) = @_; my ($self, $tfh) = @_;

local $/ = "\n"; local $/ = "\n";
local $_; local $_;
$self->{'_blastdata'} = ''; $self->{'_blastdata'} = '';

my ($sawxmlheader, $okaytoprocess); my ($sawxmlheader, $okaytoprocess);


# no buffering needed (famous last words...) # no buffering needed (famous last words...)
my $fh = $self->_fh; my $fh = $self->_fh;

#chop up XML into edible bits for the parser #chop up XML into edible bits for the parser
while( defined( my $line = <$fh>) ) { while( defined( my $line = <$fh>) ) {
if (defined $tfh) { if (defined $tfh) {
Expand Down

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