diff variant_effect_predictor/Bio/Tools/Run/WrapperBase.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Run/WrapperBase.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,354 @@
+# $Id: WrapperBase.pm,v 1.7.2.2 2003/03/11 10:52:26 jason Exp $
+#
+# BioPerl module for Bio::Tools::Run::WrapperBase
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Run::WrapperBase - A Base object for wrappers around executables
+
+=head1 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});
+
+=head1 DESCRIPTION
+
+This is a basic module from which to build executable wrapper modules.
+It has some basic methods to help when implementing new modules.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+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:
+
+  [e-mail]
+  http://bioperl.org/bioperl-bugs/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Tools::Run::WrapperBase;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::Root::RootI;
+use Bio::Root::IO;
+
+@ISA = qw(Bio::Root::RootI);
+
+=head2 run
+
+ Title   : run
+ Usage   : $wrapper->run({ARGS HERE});
+ Function: Support generic running with args passed in
+           as a hashref
+ Returns : Depends on the implementation, status OR data
+ Args    : hashref of named arguments
+
+
+=cut
+
+sub run {
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 error_string
+
+ Title   : error_string
+ Usage   : $obj->error_string($newval)
+ Function: Where the output from the last analysus run is stored.
+ Returns : value of error_string
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub error_string{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'_error_string'} = $value;
+    }
+    return $self->{'_error_string'} || '';
+}
+
+
+=head2 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)
+
+
+=cut
+
+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'};
+}
+
+=head2 save_tempfiles
+
+ Title   : save_tempfiles
+ Usage   : $obj->save_tempfiles($newval)
+ Function: 
+ Returns : value of save_tempfiles
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub save_tempfiles{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'save_tempfiles'} = $value;
+    }
+    return $self->{'save_tempfiles'};
+}
+
+=head2 outfile_name
+
+ Title   : outfile_name
+ Usage   : my $outfile = $wrapper->outfile_name();
+ Function: Get/Set the name of the output file for this run
+           (if you wanted to do something special)
+ Returns : string
+ Args    : [optional] string to set value to
+
+
+=cut
+
+sub outfile_name{
+   my ($self,$nm) = @_;
+   if( defined $nm || ! defined $self->{'_outfilename'} ) { 
+       $nm = 'mlc' unless defined $nm;
+       $self->{'_outfilename'} = $nm;
+   }
+   return $self->{'_outfilename'};
+}
+
+
+=head2 tempdir
+
+ Title   : tempdir
+ Usage   : my $tmpdir = $self->tempdir();
+ Function: Retrieve a temporary directory name (which is created)
+ Returns : string which is the name of the temporary directory
+ Args    : none
+
+
+=cut
+
+sub tempdir{
+   my ($self) = @_;
+   
+   unless( $self->{'_tmpdir'} ) {
+       $self->{'_tmpdir'} = $self->io->tempdir(CLEANUP => ! $self->save_tempfiles );
+   }
+   unless( -d $self->{'_tmpdir'} ) { 
+       mkdir($self->{'_tmpdir'},0777);
+   }
+   $self->{'_tmpdir'};
+}
+
+=head2 cleanup
+
+ Title   : cleanup
+ Usage   : $wrapper->cleanup();
+ Function: Will cleanup the tempdir directory after a PAML run
+ Returns : none
+ Args    : none
+
+
+=cut
+
+sub cleanup{
+   my ($self) = @_;
+   $self->io->_io_cleanup();
+   if( defined $self->{'_tmpdir'} &&
+       -d $self->{'_tmpdir'} ) {
+       $self->io->rmtree($self->{'_tmpdir'});
+   }
+}
+
+=head2 io
+
+ Title   : io
+ Usage   : $obj->io($newval)
+ Function: Gets a L<Bio::Root::IO> object
+ Returns : L<Bio::Root::IO> object
+ Args    : none
+
+
+=cut
+
+sub io{
+   my ($self) = @_;
+   unless( defined $self->{'io'} ) {
+       $self->{'io'} = new Bio::Root::IO(-verbose => $self->verbose());
+   }
+    return $self->{'io'};
+}
+
+=head2 version
+
+ Title   : version
+ Usage   : $version = $wrapper->version()
+ Function: Returns the program version (if available)
+ Returns : string representing version of the program 
+ Args    : [Optional] value to (re)set version string
+
+
+=cut
+
+sub version{
+   my ($self,@args) = @_;
+   return undef;
+}
+
+=head2 executable
+
+ Title   : executable
+ Usage   : my $exe = $factory->executable();
+ Function: Finds the full path to the executable
+ Returns : string representing the full path to the exe
+ Args    : [optional] name of executable to set path to
+           [optional] boolean flag whether or not warn when exe is not found
+
+=cut
+
+sub executable{
+   my ($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'};
+}
+
+=head2 program_path
+
+ Title   : program_path
+ Usage   : my $path = $factory->program_path();
+ Function: Builds path for executable 
+ Returns : string representing the full path to the exe
+ Args    : none
+
+=cut
+
+sub program_path {
+    my ($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);
+}
+
+=head2 program_dir
+
+ Title   : program_dir
+ Usage   : my $dir = $factory->program_dir();
+ Function: Abstract get method for dir of program. To be implemented
+           by wrapper.
+ Returns : string representing program directory 
+ Args    : none 
+
+=cut
+
+sub program_dir {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 program_name
+
+ Title   : program_name
+ Usage   : my $name = $factory->program_name();
+ Function: Abstract get method for name of program. To be implemented
+           by wrapper.
+ Returns : string representing program name
+ Args    : none
+
+=cut
+
+sub program_name {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+
+1;