From a27bbf8ab3ab85a2c55eda52d13d41283da2ed5e Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 17 Jun 2010 12:05:54 +0000
Subject: [PATCH] added list switch to mean_vals

git-svn-id: http://biopieces.googlecode.com/svn/trunk@989 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/mean_vals | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
index f29a4fc..44ce791 100755
--- a/bp_bin/mean_vals
+++ b/bp_bin/mean_vals
@@ -29,6 +29,7 @@
 use warnings;
 use strict;
 use Maasha::Biopieces;
+use Maasha::Calc;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -38,12 +39,16 @@ my ( $options, $in, $out, $record, $key, %sum_hash, %count_hash, $mean, $fh );
 
 $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 => 'keys',      short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { 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 => 'keys',      short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'list',      short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
     ]   
 );
 
+Maasha::Common::error( qq(both --keys and --list specified) ) if     $options->{ "keys" } and     $options->{ "list" };
+Maasha::Common::error( qq(no --keys or --list specified) )    if not $options->{ "keys" } and not $options->{ "list" };
+
 $in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
@@ -58,6 +63,11 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
         }
     }
 
+    if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } )
+    {
+        $record->{ $options->{ 'list' } . "_MEAN" } = sprintf( "%.2f", Maasha::Calc::mean( [ split ";", $record->{ $options->{ 'list' } } ] ) );
+    }
+
     Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
 }
 
-- 
2.39.2