Bio::SearchIO axt
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Summary
Bio::SearchIO::axt - a parser for axt format reports
Package variables
No package variables defined.
Included modules
Bio::Search::HSP::HSPFactory
Bio::Search::Result::ResultFactory
POSIX
Inherit
Bio::SearchIO
Synopsis
  use Bio::SearchIO;
my $parser = Bio::SearchIO->new(-format => 'axt',
-file => 't/data/report.blastz');
while( my $result = $parser->next_result ) {
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
}
}
}
Description
This is a parser and event-generator for AXT format reports. BLASTZ
reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally
in LAV format but are commonly post-processed to AXT format; many precomputed
BLASTZ reports, such as those found in the UCSC Genome
Browser, are in AXT format. This parser will also parse any
AXT format produced from any lav report and directly out of BLAT.
Methods
BEGIN Code
newDescriptionCode
next_resultDescriptionCode
_initialize
No description
Code
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
charactersDescriptionCode
_modeDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
result_countDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::SearchIO::axt->new();
Function: Builds a new Bio::SearchIO::axt object
Returns : an instance of Bio::SearchIO::axt
Args :
next_resultcodeprevnextTop
 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
start_elementcodeprevnextTop
 Title   : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
end_elementcodeprevnextTop
 Title   : start_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
elementcodeprevnextTop
 Title   : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
characterscodeprevnextTop
 Title   : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
_modecodeprevnextTop
 Title   : _mode
Usage : $obj->_mode($newval)
Function:
Example :
Returns : value of _mode
Args : newvalue (optional)
within_elementcodeprevnextTop
 Title   : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
in_elementcodeprevnextTop
 Title   : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
start_documentcodeprevnextTop
 Title   : start_document
Usage : $eventgenerator->start_document
Function: Handles a start document event
Returns : none
Args : none
end_documentcodeprevnextTop
 Title   : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
result_countcodeprevnextTop
 Title   : result_count
Usage : my $count = $searchio->result_count
Function: Returns the number of results we have processed
Returns : integer
Args : none
Methods code
BEGINTop
BEGIN {
     # mapping of NCBI Blast terms to Bioperl hash keys
%MODEMAP = ('AXTOutput' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp' ); $GAPCHAR = '-'; %MAPPING = ( 'Hsp_score' => 'HSP-score', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-hsp_gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', # ignoring this for now
'Hsp_align-len' => 'HSP-hsp_length', 'Hit_id' => 'HIT-name', 'AXTOutput_query-def'=> 'RESULT-query_name', );
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    local $/ = "\n";
    local $_;

    my ($curquery,$curhit);
    $self->start_document();
    my @hit_signifs;
    while( defined ($_ = $self->_readline )) { 
	next if (/^\s+$/);
	if( m/^(\d+)\s+      # alignment number - we'll throw this away anyways
(\S+)\s+ # Query name
(\d+)\s+(\d+)\s+ # Query start Query end (always + strand, 0 based)
(\S+)\s+ # Hit name
(\d+)\s+(\d+)\s+ # Hit start Hit end (0 based)
([\-\+])\s+ # Hit strand
([\d\.\-]+)\s+ # Score
/ox ) {
my (
$alnnum, $qname,$qstart,$qend, $hname,
$hstart,$hend,$hstrand, $score) = ($1,$2,$3,$4,$5,
$6,$7,$8,$9);
$self->{'_reporttype'} = 'AXT'; # Jim's code is 0 based
# yes, but axt format is one-based, see bug 3145 - cjfields 10-11-10
#$qstart++; $qend++; $hstart++; $hend++;
if( defined $curquery && $curquery ne $qname ) { $self->end_element({'Name' => 'Hit'}); $self->_pushback($_); $self->end_element({'Name' => 'AXTOutput'}); return $self->end_document(); } if( defined $curhit && $curhit ne $hname) { # slight duplication here -- keep these in SYNC
$self->end_element({'Name' => 'Hit'}); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hname}); } elsif ( ! defined $curquery ) { $self->start_element({'Name' => 'AXTOutput'}); $self->{'_result_count'}++; $self->element({'Name' => 'AXTOutput_query-def', 'Data' => $qname }); $self->start_element({'Name' => 'Hit'}); $self->element({'Name' => 'Hit_id', 'Data' => $hname}); } $self->start_element({'Name' => 'Hsp'}); my $queryalign = $self->_readline; my $hitalign = $self->_readline; chomp($queryalign); chomp($hitalign); my $alnlen = length($queryalign); my $qgapnum = ( $queryalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); my $hgapnum = ( $hitalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); my $totalgaps = ($qgapnum + $hgapnum); if( $hstrand eq '-' ) { # strand gets inferred by start/end
($hstart,$hend) = ($hend,$hstart); } $self->element({'Name' => 'Hsp_score', 'Data' => $score}); $self->element({'Name' => 'Hsp_query-from', 'Data' => $qstart}); $self->element({'Name' => 'Hsp_query-to', 'Data' => $qend}); $self->element({'Name' => 'Hsp_hit-from', 'Data' => $hstart}); $self->element({'Name' => 'Hsp_hit-to', 'Data' => $hend}); $self->element({'Name' => 'Hsp_gaps', 'Data' => $qgapnum + $hgapnum}); $self->element({'Name' => 'Hsp_querygaps', 'Data' => $qgapnum}); $self->element({'Name' => 'Hsp_hitgaps', 'Data' => $hgapnum}); $self->element({'Name' => 'Hsp_identity', 'Data' => $alnlen - $totalgaps}); $self->element({'Name' => 'Hsp_positive', 'Data' => $alnlen - $totalgaps}); $self->element({'Name' => 'Hsp_qseq', 'Data' => $queryalign}); $self->element({'Name' => 'Hsp_hseq', 'Data' => $hitalign}); $self->end_element({'Name' => 'Hsp'}); $curquery = $qname; $curhit = $hname; } } # fence post
if( defined $curquery ) { $self->end_element({'Name' => 'Hit'}); $self->end_element({'Name' => 'AXTOutput'}); return $self->end_document(); } return;
}
_initializedescriptionprevnextTop
sub _initialize {
    my ($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::GenericResult'));

    $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::GenericHSP'));
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($self,$data) = @_;
    # we currently don't care about attributes
my $nm = $data->{'Name'}; if( my $type = $MODEMAP{$nm} ) { $self->_mode($type); if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("start_%s",lc $type); $self->_eventHandler->$func($data->{'Attributes'}); } unshift @{$self->{'_elements'}}, $type; } if($nm eq 'AXTOutput') { $self->{'_values'} = {}; $self->{'_result'}= undef; $self->{'_mode'} = ''; }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $rc;
    # Hsp are sort of weird, in that they end when another
# object begins so have to detect this in end_element for now
if( my $type = $MODEMAP{$nm} ) { if( $self->_eventHandler->will_handle($type) ) { my $func = sprintf("end_%s",lc $type); $rc = $self->_eventHandler->$func($self->{'_reporttype'}, $self->{'_values'}); } shift @{$self->{'_elements'}}; } elsif( $MAPPING{$nm} ) { if ( ref($MAPPING{$nm}) =~ /hash/i ) { my $key = (keys %{$MAPPING{$nm}})[0]; $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'}; } else { $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'}; } } else { $self->warn( "unknown nm $nm ignoring\n"); } $self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if( $nm eq 'AXTOutput' ); return $rc;
}
elementdescriptionprevnextTop
sub element {
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}
charactersdescriptionprevnextTop
sub characters {
   my ($self,$data) = @_;   

   return unless ( defined $data->{'Data'} );
   if( $data->{'Data'} =~ /^\s+$/ ) {
       return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/;
   }

   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
       
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }  
   
   $self->{'_last_data'} = $data->{'Data'};
}
_modedescriptionprevnextTop
sub _mode {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_mode'} = $value;
    }
    return $self->{'_mode'};
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($self,$name) = @_;  
   return 0 if ( ! defined $name &&
		 ! defined  $self->{'_elements'} ||
		 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       if( $_ eq $name  ) {
	   return 1;
       } 
   }
   return 0;
}
in_elementdescriptionprevnextTop
sub in_element {
   my ($self,$name) = @_;  
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_mode'} = '';
    $self->{'_elements'} = [];
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   return $self->{'_result'};
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _