From aea17f4391d9d286d3b73649b1667aa41e3d0ca0 Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Tue, 2 Dec 2014 16:00:45 +0000
Subject: [PATCH] Work with bz2 files.
---
modules/Bio/EnsEMBL/Utils/IO.pm | 65 +++++++++++++++++++++++++++++----
1 file changed, 57 insertions(+), 8 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/IO.pm b/modules/Bio/EnsEMBL/Utils/IO.pm
index 32c9370450..5d9115cd1a 100644
--- a/modules/Bio/EnsEMBL/Utils/IO.pm
+++ b/modules/Bio/EnsEMBL/Utils/IO.pm
@@ -144,18 +144,18 @@ use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::Utils::Scalar qw(:assert);
use IO::File;
-eval {
- require IO::Compress::Bzip2;
- require IO::Uncompress::Bunzip2;
- $BZIP2_OK = 1;
-};
-
eval {
require IO::Compress::Gzip;
require IO::Uncompress::Gunzip;
$GZIP_OK = 1;
};
+eval {
+ require IO::Compress::Bzip2;
+ require IO::Uncompress::Bunzip2;
+ $BZIP2_OK = 1;
+};
+
eval {
require IO::Compress::Zip;
require IO::Uncompress::Unzip;
@@ -382,7 +382,7 @@ sub iterate_file {
-=head2 work_with_file()
+=head2 work_with_file
Arg [1] : string $file
Arg [2] : string; $mode
@@ -415,7 +415,7 @@ sub work_with_file {
return;
}
-=head2 gz_work_with_file()
+=head2 gz_work_with_file
Arg [1] : string $file
Arg [2] : string; $mode
@@ -464,6 +464,55 @@ sub gz_work_with_file {
return;
}
+=head2 bz_work_with_file
+
+ Arg [1] : string $file
+ Arg [2] : string; $mode
+ Supports modes like C<r>, C<w>, C<\>> and C<\<>
+ Arg [3] : CodeRef the callback which is given the open file handle as
+ its only argument
+ Arg [4] : HashRef used to pass options into the IO
+ compression/uncompression modules
+ Description : Performs the nitty gritty of checking if a file handle is open
+ and closing the resulting filehandle down.
+ Returntype : None
+ Example : bz_work_with_file('/tmp/out.txt.bz2', 'w', sub {
+ my ($fh) = @_;
+ print $fh 'hello';
+ return;
+ });
+ Exceptions : If we could not work with the file due to permissions
+ Status : Stable
+
+=cut
+
+sub bz_work_with_file {
+ my ($file, $mode, $callback, $args) = @_;
+ throw "IO::Compress was not available"if ! $BZIP2_OK;
+ throw "We need a file name to open" if ! $file;
+ throw "We need a mode to open the requested file with" if ! $mode;
+ assert_ref($callback, 'CODE', 'callback');
+ $args ||= {};
+
+ my $fh;
+ {
+ no warnings qw/once/;
+ if($mode =~ '>$' || $mode eq 'w') {
+ $args->{Append} = 1 if $mode =~ />>$/;
+ $fh = IO::Compress::Bzip2->new($file, %$args) or throw "Cannot open '$file' for writing: $IO::Compress::Gzip::Bzip2Error";
+ }
+ elsif($mode eq '<' || $mode eq 'r') {
+ $fh = IO::Uncompress::Bunzip2->new($file, %$args) or throw "Cannot open '$file' for writing: $IO::Uncompress::Gunzip::Bunzip2Error";
+ }
+ else {
+ throw "Could not decipher a mode from '$mode'";
+ }
+ };
+ $callback->($fh);
+ close($fh) or throw "Cannot close FH from ${file}: $!";
+ return;
+}
+
=head2 filter_dir
Arg [1] : String; directory
--
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