Bio::Tools Blat
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Summary
Bio::Tools::Blat - parser for Blat program
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic(1)
Bio::SeqFeature::Generic(2)
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
  use Bio::Tools::Blat;
my $blat_parser = Bio::Tools::Blat->new(-fh =>$filehandle );
while( my $blat_feat = $blat_parser->next_result ) {
push @blat_feat, $blat_feat;
}
Description
 Parser for Blat program
Methods
newDescriptionCode
next_resultDescriptionCode
create_featureDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Blat->new(-fh=>$filehandle);
Function: Builds a new Bio::Tools::Blat object
Returns : Bio::Tools::Blat
Args : -filename
-fh (filehandle)
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $feat = $blat_parser->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
create_featurecodeprevnextTop
 Title   : create_feature
Usage : my $feat=$blat_parser->create_feature($feature,$seqname)
Function: creates a SeqFeature Generic object
Returns : Bio::SeqFeature::Generic
Args :
Methods code
newdescriptionprevnextTop
sub new {
      my($class,@args) = @_;

      my $self = $class->SUPER::new(@args);
      $self->_initialize_io(@args);

      return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
	my ($self) = @_;
	my $filehandle;
	my $line;
	my $id;

	while ($_=$self->_readline()){
		# first split on spaces:
$line = $_; chomp $line; my ($matches, $mismatches, $rep_matches, $n_count, $q_num_insert, $q_base_insert, $t_num_insert, $t_base_insert, $strand, $q_name, $q_length, $q_start, $q_end, $t_name, $t_length, $t_start, $t_end, $block_count, $block_sizes, $q_starts, $t_starts ) = split; my $superfeature = Bio::SeqFeature::Generic->new(); # ignore any preceeding text
next unless ( $matches =~/^\d+$/ ); # create as many features as blocks there are in each output line
my (%feat1, %feat2); $feat1{name} = $t_name; $feat2{name} = $q_name; $strand = $1 if ($strand =~/([+-])[+-]/); $feat2{strand} = 1; $feat1{strand} = $strand; my $percent_id = sprintf "%.2f", (100 * ($matches + $rep_matches)/( $matches + $mismatches + $rep_matches));
unless ( $q_length ){ $self->warn("length of query is zero, something is wrong!"); next; } my $score = sprintf "%.2f", (100 * ( $matches + $mismatches + $rep_matches ) / $q_length);
# size of each block of alignment (inclusive)
my @block_sizes = split ",",$block_sizes; # start position of each block (you must add 1 as psl output
# is off by one in the start coordinate)
my @q_start_positions = split ",",$q_starts; my @t_start_positions = split ",",$t_starts; $superfeature->seq_id($q_name); $superfeature->score( $score ); $superfeature->add_tag_value('percent_id',$percent_id); # each line of output represents one possible entire aligment
# of the query (feat1) and the target(feat2)
for (my $i=0; $i<$block_count; $i++ ){ my ($query_start,$query_end); if ( $strand eq '+' ){ $query_start = $q_start_positions[$i] + 1; $query_end = $query_start + $block_sizes[$i] - 1; }else{ $query_end = $q_length - $q_start_positions[$i]; $query_start = $query_end - $block_sizes[$i] + 1; } #$feat2 {start} = $q_start_positions[$i] + 1;
#$feat2 {end} = $feat2{start} + $block_sizes[$i] - 1;
$feat2 {start} = $query_start; $feat2 {end} = $query_end; if ( $query_end < $query_start ){ $self->warn("dodgy feature coordinates: end = $query_end, start = $query_start. Reversing..."); $feat2 {end} = $query_start; $feat2 {start} = $query_end; } $feat1 {start} = $t_start_positions[$i] + 1; $feat1 {end} = $feat1{start} + $block_sizes[$i] - 1; # we put all the features with the same score and percent_id
$feat2 {score} = $score; $feat1 {score} = $feat2 {score}; $feat2 {percent} = $percent_id; $feat1 {percent} = $feat2 {percent}; # other stuff:
$feat1 {db} = undef; $feat1 {db_version} = undef; $feat1 {program} = 'blat'; $feat1 {p_version} = '1'; $feat1 {source} = 'blat'; $feat1 {primary} = 'similarity'; $feat2 {source} = 'blat'; $feat2 {primary} = 'similarity'; my $feature_pair = $self->create_feature(\%feat1,\% feat2); $superfeature->add_sub_SeqFeature( $feature_pair,'EXPAND'); } return $superfeature; }
}
create_featuredescriptionprevnextTop
sub create_feature {
    my ($self, $feat1,$feat2) = @_;
    my $feature1= Bio::SeqFeature::Generic->new(
							  -seq_id     =>$feat1->{name},
							  -start      =>$feat1->{start},
                       -end        =>$feat1->{end},
                       -strand     =>$feat1->{strand},
                       -score      =>$feat1->{score},
                       -source     =>$feat1->{source},
                       -primary    =>$feat1->{primary} );

    my $feature2= Bio::SeqFeature::Generic->new(
                       -seq_id     =>$feat2->{name},
							  -start      =>$feat2->{start},
                       -end        =>$feat2->{end},
                       -strand     =>$feat2->{strand},
                       -score      =>$feat2->{score},
                       -source     =>$feat2->{source},
                       -primary    =>$feat2->{primary} );

    my $featurepair = Bio::SeqFeature::FeaturePair->new;
    $featurepair->feature1 ($feature1);
    $featurepair->feature2 ($feature2);

	 $featurepair->add_tag_value('evalue',$feat2->{p});
	 $featurepair->add_tag_value('percent_id',$feat2->{percent});
	 $featurepair->add_tag_value("hid",$feat2->{primary});
    return  $featurepair;
}

1;
}
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 the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Balamurugan KumarasamyTop
 Email: bala@tll.org.sg
APPENDIXTop
 The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _