NAME¶
Bio::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://redmine.open-bio.org/projects/bioperl/
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
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
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
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none