From 2bae9aea07af1e58e2d8fa6ef9ade3a9c989c922 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 12 Dec 2011 11:18:26 +0000
Subject: [PATCH] removed old read_embl (perl)

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1703 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/read_embl | 99 ------------------------------------------------
 1 file changed, 99 deletions(-)
 delete mode 100755 bp_bin/read_embl

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
deleted file mode 100755
index 15ebea4..0000000
--- a/bp_bin/read_embl
+++ /dev/null
@@ -1,99 +0,0 @@
-#!/usr/bin/env perl
-
-# Copyright (C) 2007-2009 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Read EMBL entries from one or more files.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use warnings;
-use strict;
-use Storable qw( dclone );
-use Maasha::Biopieces;
-use Maasha::Filesys;
-use Maasha::EMBL;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $options, $in, $out, $data_in, $num, $entry, $record );
-
-$options = Maasha::Biopieces::parse_options(
-    [
-        { long => 'data_in',    short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
-        { long => 'num',        short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
-        { long => 'keys',       short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
-        { long => 'features',   short => 'f', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
-        { long => 'qualifiers', short => 'q', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
-    ]   
-);
-
-$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) ) {
-    Maasha::Biopieces::put_record( $record, $out );
-}
-
-if ( $options->{ 'data_in' } )
-{
-    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
-
-    $num = 1;
-
-    while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) ) 
-    {
-        map { Maasha::Biopieces::put_record( $_, $out ) } Maasha::EMBL::embl2biopieces( $entry, $options );
-
-        last if $options->{ "num" } and $num == $options->{ "num" };
-
-        $num++;
-    }
-
-    close $data_in;
-}
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-BEGIN
-{
-    Maasha::Biopieces::status_set();
-}
-
-
-END
-{
-    Maasha::Biopieces::status_log();
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__
-- 
2.39.5