X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fmedian_vals;h=e32415ca05094bb872cf4d193c70fbae1e378a52;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=9428f9a2efd18dbaa6596f032c6178cdc04dcd2d;hpb=b607bb9d6e4adcebd9f9e128aacc91a212010ee0;p=biopieces.git

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
index 9428f9a..e32415c 100755
--- a/bp_bin/median_vals
+++ b/bp_bin/median_vals
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Calc;
@@ -34,16 +35,20 @@ use Maasha::Calc;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $record, $key, %median_hash, $median, $fh );
+my ( $options, $in, $out, $record, $new_record, $key, %median_hash, $median, $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" } );
 
@@ -53,9 +58,16 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
         push @{ $median_hash{ $key } }, $record->{ $key } if defined $record->{ $key };
     }
 
+    if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) {
+        $record->{ $options->{ 'list' } . "_MEDIAN" } = sprintf( "%.2f", Maasha::Calc::median( [ 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" } } )
@@ -66,7 +78,14 @@ foreach $key ( @{ $options->{ "keys" } } )
         $median = "N/A";
     }
 
-    Maasha::Biopieces::put_record( { $key . "_MEDIAN" => $median } , $fh );
+    $new_record->{ $key . "_MEDIAN" } = $median;
+}
+
+if ( $options->{ "keys" } and $new_record )
+{
+    $new_record->{ 'REC_TYPE' } = "MEDIAN";
+
+    Maasha::Biopieces::put_record( $new_record, $fh );
 }
 
 close $fh;
@@ -77,20 +96,13 @@ close $fh;
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -98,4 +110,3 @@ END
 
 
 __END__
-