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Bio::Tools::TandemRepeatsFinder.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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