Bio::Tools::Run::RepeaUserkContributed Perl DoBio::Tools::Run::RepeatMasker(3)NAMEBio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program
SYNOPSIS
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;
DESCRIPTION
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;
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 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
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
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a "_".
program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
new
Title : new
Usage : $rm->new($seq)
Function: creates a new wrapper
Returns: Bio::Tools::Run::RepeatMasker
Args : self
version
Title : version
Usage :
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
run
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
mask
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
_run
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
masked_seq
Title : masked_seq
Usage : $rm->masked_seq($seq)
Function: get/set for masked sequence
Example :
Returns : the masked sequence
Args : Bio::Seq object
repeat_features
Title : repeat_features
Usage : $rm->repeat_features(\@rf)
Function: get/set for repeat features array
Example :
Returns : the array of repeat features
Args :
_setparams()
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
_setinput()
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
Bio::Tools::Run::Wrapper methods
no_param_checks
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)
save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_name
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
tempdir
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
cleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
perl v5.14.1 2011-07-21 Bio::Tools::Run::RepeatMasker(3)
