bzip2 based array slurping and corresponding tests.

modules/Bio/EnsEMBL/Utils/IO.pm

@@ -317,14 +317,14 @@ sub slurp_to_array {
 	return $contents;
 }
 
-=head2 gz_slurp_to_array()
+=head2 gz_slurp_to_array
 
   Arg [1]     : string $file
   Arg [2]     : boolean $chomp
   Arg [3]     : HashRef arguments to pass into IO compression layers
   Description : Sends the contents of the given gzipped file into an ArrayRef
   Returntype  : ArrayRef
-  Example     : my $contents_array = slurp_to_array('/tmp/file.txt.gz');
+  Example     : my $contents_array = gz_slurp_to_array('/tmp/file.txt.gz');
   Exceptions  : If the file did not exist or was not readable
   Status      : Stable
 
@@ -341,7 +341,31 @@ sub gz_slurp_to_array {
   return $contents;
 }
 
-=head2 fh_to_array()
+=head2 bz_slurp_to_array
+
+  Arg [1]     : string $file
+  Arg [2]     : boolean $chomp
+  Arg [3]     : HashRef arguments to pass into IO compression layers
+  Description : Sends the contents of the given bzipped file into an ArrayRef
+  Returntype  : ArrayRef
+  Example     : my $contents_array = bz_slurp_to_array('/tmp/file.txt.bz2');
+  Exceptions  : If the file did not exist or was not readable
+  Status      : Stable
+
+=cut
+
+sub bz_slurp_to_array {
+  my ($file, $chomp, $args) = @_;
+  my $contents;
+  bz_work_with_file($file, 'r', sub {
+    my ($fh) = @_;
+    $contents = fh_to_array($fh, $chomp);
+    return;
+  }, $args);
+  return $contents;
+}
+
+=head2 fh_to_array
 
   Arg [1]     : Glob/IO::Handle $fh
   Arg [2]     : boolean $chomp

modules/t/io.t

@@ -69,6 +69,12 @@ SKIP: {
   my $content = bz_slurp($bz2tmpfile->filename);
   like($content, qr/test data/, "Bzip2: correct content");
   like($content, qr/more data/, "Bzip2: more correct content");
+
+  # test bz_slurp_to_array
+  my $content_array = bz_slurp_to_array($bz2tmpfile->filename, 1);
+  ok($content_array->[0] eq 'test data', "Bzip2 slurped file first element");
+  ok($content_array->[1] eq 'some more data.', "Bzip2 slurped file second element");
+
 }
 
 my $ZIP_OK = 0;
@@ -80,12 +86,12 @@ eval {
 
 SKIP: {
   skip "Cannot run Zip/Unzip tests, install related IO::[Un]Compress modules first",
-    2 unless $BZIP2_OK;
+    2 unless $ZIP_OK;
 
   # send the content of the tmpfile to another
   # bzip2 compressed file
   my $file_content = slurp($tmpfilename);
-  my $bz2tmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.bz2');
+  my $bz2tmpfile = File::Temp->new(DIR => $dirname, SUFFIX => '.zip');
 
   zip_work_with_file($bz2tmpfile->filename, 'w', sub {
     my ($fh) = @_;
@@ -97,6 +103,7 @@ SKIP: {
   my $content = zip_slurp($bz2tmpfile->filename);
   like($content, qr/test data/, "Zip: correct content");
   like($content, qr/more data/, "Zip: more correct content");
+
 }