From e481c33c8674058258da9b5f2ff9165a78d6c65a Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 21 Oct 2009 14:34:27 +0000
Subject: [PATCH] added kiss biopieces

git-svn-id: http://biopieces.googlecode.com/svn/trunk@701 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/read_kiss  | 96 +++++++++++++++++++++++++++++++++++++++++++++++
 bp_bin/write_kiss | 86 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 182 insertions(+)
 create mode 100755 bp_bin/read_kiss
 create mode 100755 bp_bin/write_kiss

diff --git a/bp_bin/read_kiss b/bp_bin/read_kiss
new file mode 100755
index 0000000..043f08a
--- /dev/null
+++ b/bp_bin/read_kiss
@@ -0,0 +1,96 @@
+#!/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 FASTA entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::KISS::IO;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_in, $num, $entry );
+
+$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' },
+    ]   
+);
+
+$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::KISS::IO::kiss_entry_get( $data_in ) ) 
+    {
+        if ( $record = Maasha::KISS::IO::kiss2biopiece( $entry ) ) {
+            Maasha::Biopieces::put_record( $record, $out );
+        }
+
+        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__
diff --git a/bp_bin/write_kiss b/bp_bin/write_kiss
new file mode 100755
index 0000000..dec6238
--- /dev/null
+++ b/bp_bin/write_kiss
@@ -0,0 +1,86 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write KISS entries from stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::KISS::IO;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $fh, $record, $entry, $new_record );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'data_out',  short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'compress',  short => 'Z', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ 'data_out' }, $options->{ 'compress' } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $entry = Maasha::KISS::IO::biopiece2kiss( $record ) ) {
+        Maasha::KISS::IO::kiss_entry_put( $entry, $fh );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };
+}
+
+close $fh;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-- 
2.39.2