| Bio::Tools::Run::RepeatMasker(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::RepeatMasker(3pm) |
Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program
use Bio::Tools::Run::RepeatMasker;
my @params=("mam" => 1,"noint"=>1);
my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
$in = Bio::SeqIO->new(-file => "contig1.fa",
-format => 'fasta');
my $seq = $in->next_seq();
#return an array of Bio::SeqFeature::FeaturePair objects
my @feats = $factory->run($seq);
# or
$factory->run($seq);
my @feats = $factory->repeat_features;
#return the masked sequence, a Bio::SeqI object
my $masked_seq = $factory->run;
To use this module, the RepeatMasker program (and probably database) must be installed. RepeatMasker is a program that screens DNA sequences for interspersed repeats known to exist in mammalian genomes as well as for low complexity DNA sequences. For more information, on the program and its usage, please refer to http://www.repeatmasker.org/.
Having installed RepeatMasker, you must let Bioperl know where it is. This can be done in (at least) three ways:
1. Make sure the RepeatMasker executable is in your path.
2. Define an environmental variable REPEATMASKERDIR which is a
directory which contains the RepeatMasker executable:
In bash:
export REPEATMASKERDIR=/home/username/RepeatMasker/
In csh/tcsh:
setenv REPEATMASKERDIR /home/username/RepeatMasker/
3. Include a definition of an environmental variable REPEATMASKERDIR in
every script that will use this RepeatMasker wrapper module, e.g.:
BEGIN { $ENV{REPEATMASKERDIR} = '/home/username/RepeatMasker/' }
use Bio::Tools::Run::RepeatMasker;
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/
Email shawnh@fugu-sg.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
Title : new Usage : $rm->new($seq) Function: creates a new wrapper Returns: Bio::Tools::Run::RepeatMasker Args : self
Title : version Usage : Function: Determine the version number of the program Example : Returns : float or undef Args : none
Title : run
Usage : $rm->run($seq);
Function: Run Repeatmasker on the sequence set as
the argument
Returns : an array of repeat features that are
Bio::SeqFeature::FeaturePairs
Args : Bio::PrimarySeqI compliant object
Title : mask
Usage : $rm->mask($seq)
Function: This method is deprecated. Call run() instead
Example :
Returns : an array of repeat features that are
Bio::SeqFeature::FeaturePairs
Args : Bio::PrimarySeqI compliant object
Title : _run Usage : $rm->_run ($filename,$param_string) Function: internal function that runs the repeat masker Example : Returns : an array of repeat features Args : the filename to the input sequence and the parameter string
Title : masked_seq Usage : $rm->masked_seq($seq) Function: get/set for masked sequence Example : Returns : the masked sequence Args : Bio::Seq object
Title : repeat_features Usage : $rm->repeat_features(\@rf) Function: get/set for repeat features array Example : Returns : the array of repeat features Args :
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for repeatmasker program Example : Returns : parameter string to be passed to repeatmasker Args : name of calling object
Title : _setinput Usage : Internal function, not to be called directly Function: writes input sequence to file and return the file name Example : Returns : string Args : a Bio::PrimarySeqI compliant object
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
Title : outfile_name
Usage : my $outfile = $codeml->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none
Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none
| 2023-01-22 | perl v5.36.0 |