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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Pipeline/FASTA/Indexer.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,58 @@
+package Bio::EnsEMBL::Pipeline::FASTA::Indexer;
+
+use strict;
+use warnings;
+
+use base qw/Bio::EnsEMBL::Pipeline::FASTA::Base/;
+
+use File::Copy qw/copy/;
+use File::Spec;
+use Bio::EnsEMBL::Utils::Exception qw/throw/;
+
+sub decompress {
+  my ($self) = @_;
+  my $source = $self->param('file');
+  my $target_dir = $self->target_dir();
+  my ($vol, $dir, $file) = File::Spec->splitpath($source);
+  my $target = File::Spec->catdir($target_dir, $file);
+  my $gunzipped_target = $target;
+  $gunzipped_target =~ s/.gz$//;
+  $self->info('Copying from %s to %s', $source, $target);
+  copy($source, $target) or throw "Cannot copy $source to $target: $!";
+  $self->info('Decompressing %s to %s', $source, $gunzipped_target);
+  system("gunzip -f $target") and throw sprintf('Could not gunzip. Exited with code %d', ($? >>8));
+  return $gunzipped_target;
+}
+
+sub repeat_mask_date {
+  my ($self) = @_;
+  my $res = $self->get_DBAdaptor()->dbc()->sql_helper()->execute_simple(
+    -SQL => <<'SQL',
+select max(date_format( created, "%Y%m%d"))
+from analysis a join meta m on (a.logic_name = lower(m.meta_value))
+where meta_key =?
+SQL
+    -PARAMS => ['repeat.analysis']
+  );
+  return $res->[0] if @$res;
+  return q{};
+}
+
+sub run {
+  my ($self) = @_;
+  my $decompressed = $self->decompress();
+  $self->index_file($decompressed);
+  $self->cleanup_DBAdaptor();
+  return;
+}
+
+sub index_file {
+  die "Implement";
+}
+
+sub target_dir {
+  die "Implement";
+}
+
+
+1;