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