Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output

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

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 - Eric Just

       Email e-just@northwestern.edu

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        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

   version
        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_id
        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_description
        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_parameters
        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_result
        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_feature
        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