| Bio::Tools::TandemRepeatsFinder(3pm) | User Contributed Perl Documentation | Bio::Tools::TandemRepeatsFinder(3pm) |
Bio::Tools::TandemRepeatsFinder - a parser for Tandem Repeats Finder output
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";
}
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
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
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.
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
Email e-just@northwestern.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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)
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)
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)
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)
Title : next_result Usage : my $r = $trf->next_result() Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none
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
| 2020-10-28 | perl v5.30.3 |