diff variant_effect_predictor/Bio/EnsEMBL/Pipeline/FindDirs.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Pipeline/FindDirs.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,80 @@
+=pod
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Pipeline::FindDirs
+
+=head1 DESCRIPTION
+
+Finds all directories under the given path.
+
+Allowed parameters are:
+
+=over 8
+
+=item path - The path to search
+
+=back
+
+=cut
+
+package Bio::EnsEMBL::Pipeline::FindDirs;
+
+use strict;
+use warnings;
+
+use base qw/Bio::EnsEMBL::Hive::RunnableDB::JobFactory/;
+
+use File::Spec;
+
+sub fetch_input {
+  my ($self) = @_;
+  $self->throw("No 'path' parameter specified") unless $self->param('path');
+  my $dirs = $self->dirs();
+  $self->param('inputlist', $dirs);
+  return;
+}
+
+sub dirs {
+  my ($self) = @_;
+  
+  my @dirs;
+  
+  my $dir = $self->param('path');
+  $self->info('Searching directory %s', $dir);
+
+  opendir(my $dh, $dir) or die "Cannot open directory $dir";
+  my @files = sort { $a cmp $b } readdir($dh);
+  closedir($dh) or die "Cannot close directory $dir";
+
+  foreach my $file (@files) {
+    next if $file =~ /^\./;         #hidden file or up/current dir
+    my $path = File::Spec->catdir($dir, $file);
+    if(-d $path) {
+      $self->fine('Adding %s to the list of found dirs', $path);
+      push(@dirs, $path);
+    }
+  }
+  
+  return \@dirs;
+}
+
+1;