refactoring of assemble_pairs

[biopieces.git] / bp_bin / mean_vals

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
index 654c4fe337de2c41ac7d8ab62bbe47a9cd3c3ae9..974c9b4de1a53b64cbe46538f9c820f4ceab97ef 100755 (executable)
--- a/bp_bin/mean_vals
+++ b/bp_bin/mean_vals
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,23 +26,29 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
+use Maasha::Calc;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $record, $key, %sum_hash, %count_hash, $mean, $fh );
+my ( $options, $in, $out, $record, $new_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" } );
 
@@ -57,9 +63,16 @@ 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" };
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
 
 foreach $key ( @{ $options->{ "keys" } } )
@@ -70,13 +83,17 @@ foreach $key ( @{ $options->{ "keys" } } )
         $mean = "N/A";
     }
 
-    Maasha::Biopieces::put_record( { $key . "_MEAN" => $mean } , $fh );
+    $new_record->{ $key . "_MEAN" } = $mean
 }
 
-close $fh;
+if ( $options->{ "keys" } and $new_record )
+{
+    $new_record->{ 'REC_TYPE' } = "MEAN";
 
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
+    Maasha::Biopieces::put_record( $new_record, $fh );
+}
+
+close $fh;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<