X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fmin_vals;h=11410e3f68d7f726351544c04981e2996f8d7157;hb=2f0fd91b461033529a4a72e161bd133252a22eb6;hp=34024b1fd2ef1a911ea4468a310e092ae6b5801a;hpb=b607bb9d6e4adcebd9f9e128aacc91a212010ee0;p=biopieces.git

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
index 34024b1..11410e3 100755
--- a/bp_bin/min_vals
+++ b/bp_bin/min_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, $fh, %min_hash, $min_record );
+my ( $options, $in, $out, $record, $new_record, $key, $fh, %min_hash );
 
 $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" } );
 
@@ -60,17 +66,28 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
         }
     }
 
+    if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) {
+        $record->{ $options->{ 'list' } . "_MIN" } = sprintf( "%.2f", Maasha::Calc::list_min( [ 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" } } )
-{
-    $min_record->{ $key . "_MIN" } = $min_hash{ $key };
+foreach $key ( @{ $options->{ "keys" } } ) {
+    $new_record->{ $key . "_MIN" } = $min_hash{ $key };
 }
 
-Maasha::Biopieces::put_record( $min_record, $fh );
+if ( $options->{ "keys" } and $new_record )
+{
+    $new_record->{ 'REC_TYPE' } = "MIN";
+
+    Maasha::Biopieces::put_record( $new_record, $fh );
+}
 
 close $fh;
 
@@ -80,20 +97,13 @@ 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();
 }
 
 
@@ -101,4 +111,3 @@ END
 
 
 __END__
-