Bio::Tools::Run
WrapperBase
Summary
Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# do not use this object directly, it provides the following methods
# for its subclasses
my $errstr = $obj->error_string();
my $exe = $obj->executable();
$obj->save_tempfiles($booleanflag)
my $outfile= $obj->outfile_name();
my $tempdir= $obj->tempdir(); # get a temporary dir for executing
my $io = $obj->io; # Bio::Root::IO object
my $cleanup= $obj->cleanup(); # remove tempfiles
$obj->run({-arg1 => $value});
Description
This is a basic module from which to build executable wrapper modules.
It has some basic methods to help when implementing new modules.
Methods
Methods description
Title : run
Usage : $wrapper->run({ARGS HERE});
Function: Support generic running with args passed in
as a hashref
Returns : Depends on the implementation, status OR data
Args : hashref of named arguments |
Title : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysis run is stored.
Returns : value of error_string
Args : newvalue (optional) |
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 = $wrapper->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 : $wrapper->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none |
Title : version
Usage : $version = $wrapper->version()
Function: Returns the program version (if available)
Returns : string representing version of the program
Args : [Optional] value to (re)set version string |
Title : executable
Usage : my $exe = $factory->executable();
Function: Finds the full path to the executable
Returns : string representing the full path to the exe
Args : [optional] name of executable to set path to
[optional] boolean flag whether or not warn when exe is not found |
Title : program_path
Usage : my $path = $factory->program_path();
Function: Builds path for executable
Returns : string representing the full path to the exe
Args : none |
Title : program_dir
Usage : my $dir = $factory->program_dir();
Function: Abstract get method for dir of program. To be implemented
by wrapper.
Returns : string representing program directory
Args : none |
Title : program_name
Usage : my $name = $factory->program_name();
Function: Abstract get method for name of program. To be implemented
by wrapper.
Returns : string representing program name
Args : none |
Methods code
sub run
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub error_string
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'_error_string'} = $value;
}
return $self->{'_error_string'} || '';} | sub no_param_checks
{ my ($self,$value) = @_;
if( defined $value || ! defined $self->{'no_param_checks'} ) {
$value = 0 unless defined $value;
$self->{'no_param_checks'} = $value;
}
return $self->{'no_param_checks'};} | sub save_tempfiles
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'save_tempfiles'} = $value;
}
return $self->{'save_tempfiles'};} | sub outfile_name
{ my ($self,$nm) = @_;
if( defined $nm || ! defined $self->{'_outfilename'} ) {
$nm = 'mlc' unless defined $nm;
$self->{'_outfilename'} = $nm;
}
return $self->{'_outfilename'};} | sub tempdir
{ my ($self) = @_;
unless( $self->{'_tmpdir'} ) {
$self->{'_tmpdir'} = $self->io->tempdir(CLEANUP => ! $self->save_tempfiles );
}
unless( -d $self->{'_tmpdir'} ) {
mkdir($self->{'_tmpdir'},0777);
}
$self->{'_tmpdir'};} | sub cleanup
{ my ($self) = @_;
$self->io->_io_cleanup();
if( defined $self->{'_tmpdir'} &&
-d $self->{'_tmpdir'} ) {
$self->io->rmtree($self->{'_tmpdir'});
}} | sub io
{ my ($self) = @_;
unless( defined $self->{'io'} ) {
$self->{'io'} = new Bio::Root::IO(-verbose => $self->verbose());
}
return $self->{'io'};} | sub version
{ my ($self,@args) = @_;
return undef; } | sub executable
{ my ($self, $exe,$warn) = @_;
if( defined $exe ) {
$self->{'_pathtoexe'} = $exe;
}
unless( defined $self->{'_pathtoexe'} ) {
my $prog_path = $self->program_path;
if( $prog_path && -e $prog_path && -x $prog_path ) {
$self->{'_pathtoexe'} = $prog_path;
} else {
my $exe;
if( ( $exe = $self->io->exists_exe($self->program_name) ) &&
-x $exe ) {
$self->{'_pathtoexe'} = $exe;
} else {
$self->warn("Cannot find executable for ".$self->program_name) if $warn;
$self->{'_pathtoexe'} = undef;
}
}
}
$self->{'_pathtoexe'};} | sub program_path
{ my ($self) = @_;
my @path;
push @path, $self->program_dir if $self->program_dir;
push @path, $self->program_name.($^O =~ /mswin/i ?'.exe':'');
return Bio::Root::IO->catfile(@path);} | sub program_dir
{ my ($self) = @_;
$self->throw_not_implemented();} | sub program_name
{ my ($self) = @_;
$self->throw_not_implemented();} | sub DESTROY
{ my $self= shift;
unless ( $self->save_tempfiles ) {
$self->cleanup();
}
$self->SUPER::DESTROY();} | General documentation
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/MailList.shtml - About the mailing lists
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
email or the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/
| AUTHOR - Jason Stajich | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _