refactoring of assemble_pairs

[biopieces.git] / bp_bin / split_vals

diff --git a/bp_bin/split_vals b/bp_bin/split_vals
index a510c58f8ef41a6b70fe384b657ea11fa4d344d9..93cac4a118b087f485c8c5d44b06b6545ce26a8a 100755 (executable)
--- a/bp_bin/split_vals
+++ b/bp_bin/split_vals
@@ -1,52 +1,67 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
 
-use strict;
-use Data::Dumper;
-use Time::HiRes qw( gettimeofday );
-use Getopt::Long qw( :config bundling );
-use Maasha::Biopieces;
 
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Split the values of a key into new key/value pairs.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $script, $t0, $t1, %options, $in, $out, $record, @vals, $i );
+use warnings;
+use strict;
+use Maasha::Biopieces;
+
 
-$t0 = Time::HiRes::gettimeofday();
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-$script = ( split "/", $0 )[ -1 ];
 
-Maasha::Biopieces::log_biopiece();
+my ( $options, $in, $out, $record, @vals, $i );
 
-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' } };
-    
-        for ( $i = 0; $i < @vals; $i++ )
+        @vals = split /$options->{ 'delimit' }/, $record->{ $options->{ 'key' } };
+
+        if ( scalar @vals > 1 )
         {
-            if ( defined $options{ "keys" } and defined $options{ "keys" }->[ $i ] ) {
-                $record->{ $options{ "keys" }->[ $i ] } = $vals[ $i ];
-            } else {
-                $record->{ $options{ 'key' } . "_$i" } = $vals[ $i ];
+            for ( $i = 0; $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 ];
+                }
             }
         }
     }
@@ -54,13 +69,26 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
-$t1 = Time::HiRes::gettimeofday();
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
 
-print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) ) if $options{ 'verbose' };
+END
+{
+    Maasha::Biopieces::status_log();
+}
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 __END__
-