Bio::Tools::TandemRepeatsFinder(3pm) User Contributed Perl Documentation 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 $feat->seq_id()." ".$feat->start()." ".$feat->end()." $percent_matches $consensus_sequence
";
}
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://redmine.open-bio.org/projects/bioperl/
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 v5.14.2 2012-03-02 Bio::Tools::TandemRepeatsFinder(3pm)