polishing split_vals

git-svn-id: http://biopieces.googlecode.com/svn/trunk@380 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/split_vals b/bp_bin/split_vals
index a510c58f8ef41a6b70fe384b657ea11fa4d344d9..fdb06ced0e89f4100fc2dc94a268b1d10988ff7d 100755 (executable)
--- a/bp_bin/split_vals
+++ b/bp_bin/split_vals
@@ -1,52 +1,41 @@
 #!/usr/bin/env perl -w
 
 use strict;
-use Data::Dumper;
-use Time::HiRes qw( gettimeofday );
-use Getopt::Long qw( :config bundling );
 use Maasha::Biopieces;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $script, $t0, $t1, %options, $in, $out, $record, @vals, $i );
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @vals, $i );
 
-$t0 = Time::HiRes::gettimeofday();
-
-$script = ( split "/", $0 )[ -1 ];
+$run_time_beg = Maasha::Biopieces::run_time();
 
 Maasha::Biopieces::log_biopiece();
 
-GetOptions(
-    \%options,
-    'key|k=s',
-    'keys|K=s',
-    'delimit|d=s',
-    'stream_in|I=s',
-    'stream_out|O=s',
-    'verbose|v',
-    'help|?'
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'key',     short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'keys',    short => 'K', type => 'list',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'delimit', short => 'd', type => 'string', mandatory => 'no',  default => '_',   allowed => undef, disallowed => undef },
+    ]   
 );
 
-$options{ "keys" }    = [ split ",", $options{ "keys" } ] if defined $options{ "keys" };
-$options{ "delimit" } = '_' if not defined $options{ "delimit" };
-
-$in  = Maasha::Biopieces::read_stream( $options{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options{ "stream_out" } );
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
-    if ( exists $options{ 'key' } and exists $record->{ $options{ 'key' } } )
+    if ( exists $options->{ 'key' } and exists $record->{ $options->{ 'key' } } )
     {
-        @vals = split /$options{ 'delimit' }/, $record->{ $options{ 'key' } };
+        @vals = split /$options->{ 'delimit' }/, $record->{ $options->{ 'key' } };
     
         for ( $i = 0; $i < @vals; $i++ )
         {
-            if ( defined $options{ "keys" } and defined $options{ "keys" }->[ $i ] ) {
-                $record->{ $options{ "keys" }->[ $i ] } = $vals[ $i ];
+            if ( defined $options->{ "keys" } and defined $options->{ "keys" }->[ $i ] ) {
+                $record->{ $options->{ "keys" }->[ $i ] } = $vals[ $i ];
             } else {
-                $record->{ $options{ 'key' } . "_$i" } = $vals[ $i ];
+                $record->{ $options->{ 'key' } . "_$i" } = $vals[ $i ];
             }
         }
     }
@@ -54,9 +43,12 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
-$t1 = Time::HiRes::gettimeofday();
+close $in;
+close $out;
+
+$run_time_end = Maasha::Biopieces::run_time();
 
-print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) ) if $options{ 'verbose' };
+Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<