Bio::Tools TandemRepeatsFinder
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
    use Bio::Tools::TandemRepeatsFinder;
# create parser my $parser = Bio::Tools::Bio::Tools::TandemRepeatsFinder->new(-file => 'tandem_repeats.out'); # loop through results while( my $feature = $parser->next_result ) { # print the source sequence id, start, end, percent matches, and the consensus sequence my ($percent_matches) = $feat->get_tag_values('percent_matches'); my ($consensus_sequence) = $feat->get_tag_values('consensus_sequence'); print $feat->seq_id()."\t".$feat->start()."\t".$feat->end()."\t$percent_matches\t$consensus_sequence\n"; }
Description
A parser for Tandem Repeats Finder output.
Written and tested for version 4.00
Location, seq_id, and score are stored in Bio::SeqFeature::Generic feature.
All other data is stored in tags. The availabale tags are
        period_size
copy_number
consensus_size
percent_matches
percent_indels
percent_a
percent_c
percent_g
percent_t
entropy
consensus_sequence
repeat_sequence
run_parameters
sequence_description
The run_parameters are stored in a hashref with the following key:
        match_weight
mismatch_weight
indel_weight
match_prob
indel_prob
min_score
max_period_size
Methods
newDescriptionCode
versionDescriptionCode
_current_seq_idDescriptionCode
_current_seq_descriptionDescriptionCode
_current_parametersDescriptionCode
next_resultDescriptionCode
_create_featureDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::TandemRepeatsFinder->new();
Function: Builds a new Bio::Tools::TandemRepeatsFinder object
Returns : Bio::Tools::TandemRepeatsFinder
Args : -fh/-file => $val, for initing input, see Bio::Root::IO
versioncodeprevnextTop
 Title   : version
Usage : $self->version( $version )
Function: get/set the version of Tandem Repeats finder that was used in analysis
Returns : value of version of
Args : new value (optional)
_current_seq_idcodeprevnextTop
 Title   : _current_seq_id
Usage : $self->_current_seq_id( $current_seq_id )
Function: get/set the _current_seq_id
Returns : value of _current_seq_id
Args : new value (optional)
_current_seq_descriptioncodeprevnextTop
 Title   : _current_seq_description
Usage : $self->_current_seq_description( $current_seq_id )
Function: get/set the _current_seq_description
Returns : value of _current_seq_description
Args : new value (optional)
_current_parameterscodeprevnextTop
 Title   : _current_parameters
Usage : $self->_current_parameters( $parameters_hashref )
Function: get/set the _current_parameters
Returns : hashref representing current parameters parsed from results file
: keys are
match_weight
mismatch_weight
indel_weight
match_prob
indel_prob
min_score
max_period_size
Args : parameters hashref (optional)
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $r = $trf->next_result()
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
_create_featurecodeprevnextTop
 Title   : _create_feature
Usage : internal method used by 'next_feature'
Function: Takes a line from the results file and creates a bioperl object
Returns : Bio::SeqFeature::Generic
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ( $class, @args ) = @_;

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

    return $self;
}
versiondescriptionprevnextTop
sub version {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'version'} = $value;
    }
    return $self->{'version'};
}
_current_seq_iddescriptionprevnextTop
sub _current_seq_id {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_current_seq_id'} = $value;
    }
    return $self->{'_current_seq_id'};
}
_current_seq_descriptiondescriptionprevnextTop
sub _current_seq_description {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_current_seq_description'} = $value;
    }
    return $self->{'_current_seq_description'};
}
_current_parametersdescriptionprevnextTop
sub _current_parameters {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_current_parameters'} = $value;
    }
    return $self->{'_current_parameters'};
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    while ( defined( $_ = $self->_readline() ) ) {

        # Parse Version line
if (/^Version (.+)/) { my $version = $1; $self->warn("parsed version: $version\n") if DEBUG; $self->warn( qq{ Bio::Tools::TandemRepeatsFinder was written and tested for Tandem Repeats Masker Version 4.00 output You appear to be using Verion $version. Use at your own risk.}) if ($version != 4); $self->version($version); } # Parse Sequence identifier
# i.e. Sequence: DDB0215018 |Masked Chromosomal Sequence| Chr 2f
elsif ( /^Sequence: ([^\s]+)\s(.+)?/ ) { my $seq_id = $1; my $seq_description = $2; $self->warn("parsed sequence_id: $seq_id\n") if DEBUG; $self->_current_seq_id($seq_id); $self->_current_seq_description($seq_description); } # Parse Parameters
# i.e. Parameters: 2 7 7 80 10 50 12
elsif (/^Parameters: (.+)/) { my $params = $1; $self->warn("parsed parameters: $params\n") if DEBUG; my @param_array = split /\s/, $params; my $param_hash = { match_weight => $param_array[0], mismatch_weight => $param_array[1], indel_weight => $param_array[2], match_prob => $param_array[3], indel_prob => $param_array[4], min_score => $param_array[5], max_period_size => $param_array[6] }; $self->_current_parameters($param_hash); } # Parse Data
# i.e. 13936 13960 12 2.1 12 100 0 50 16 8 52 24 1.70 T TTTTTTTTTT
elsif (/^\d+\s\d+\s\d+/) { # call internal method to create Bio::SeqFeature::Generic
# to represent tandem repeat
return $self->_create_feature($_); } elsif (DEBUG) { $self->warn( "UNPARSED LINE:\n" . $_ ); } } return;
}
_create_featuredescriptionprevnextTop
sub _create_feature {
    my ( $self, $line ) = @_;

    # split the line and store into named variables
my @element = split /\s/, $line; my ( $start, $end, $period_size, $copy_number, $consensus_size, $percent_matches, $percent_indels, $score, $percent_a, $percent_c, $percent_g, $percent_t, $entropy, $consensus_sequence, $repeat_sequence ) = @element; # create tag hash from data in line
my $tags = { period_size => $period_size, copy_number => $copy_number, consensus_size => $consensus_size, percent_matches => $percent_matches, percent_indels => $percent_indels, percent_a => $percent_a, percent_c => $percent_c, percent_g => $percent_g, percent_t => $percent_t, entropy => $entropy, consensus_sequence => $consensus_sequence, repeat_sequence => $repeat_sequence, run_parameters => $self->_current_parameters(), sequence_description => $self->_current_seq_description() }; # create feature from start/end etc
my $feat = Bio::SeqFeature::Generic->new( -seq_id => $self->_current_seq_id(), -score => $score, -start => $start, -end => $end, -source_tag => 'Tandem Repeats Finder', -primary_tag => 'tandem repeat', -tag => $tags ); return $feat; } 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 via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Eric JustTop
Email e-just@northwestern.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _