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Bio::Tools::TandemRepeUseriContributed Perl Bio::Tools::TandemRepeatsFinder(3)

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	available 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

perl v5.32.1			  2019-12-07Bio::Tools::TandemRepeatsFinder(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Eric Just | APPENDIX

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