Changeset 22808

Timestamp:

08/09/10 21:37:13 (17 months ago)

Author:

alex

Message:

Updated perl example outline

File:

• trunk/bio/tutorial/malariamine/examples/kegg-to-items-example (modified) (2 diffs)

trunk/bio/tutorial/malariamine/examples/kegg-to-items-example

@@ -3 +3 @@
 use warnings;
 use strict;
+use lib '/../intermine/perl/lib';
 
-BEGIN {
-  push (@INC, ($0 =~ m:(.*)/.*:)[0] . '/../intermine/perl/lib');
+use XML::Writer;
+use InterMine::Model;
+use InterMine::ItemFactory;
+
+if (@ARGV != 4) {
+  die "usage: $0 model_file kegg_map_title_file kegg_gene_map out_file\n";
 }
 
-use XML::Writer;
-use InterMine::Item;
-use InterMine::ItemFactory;
-use InterMine::Model;
-
-if (@ARGV != 3) {
-  die "usage: $0 model_file kegg_map_title_file kegg_gene_map\n";
-}
-
-my ($model_file, $map_title_filename, $gene_map_filename) = @ARGV;
+my ($model_file, $map_title_filename, $gene_map_filenamei, $outfile) = @ARGV;
 
 my $data_source = 'Kegg';
-my $taxon_id = 36329;
-
-my @items = ();
-
+my $taxon_id    = 36329;
 
 # The item factory needs the model so that it can check that new objects have
 # valid classnames and fields
-my $model = new InterMine::Model(file => $model_file);
-my $item_factory = new InterMine::ItemFactory(model => $model);
+my $model        = InterMine::Model->new(file => $model_file);
+my $item_factory = InterMine::ItemFactory->new(model => $model);
 
+my @items;
 
 # read the map title file into %pathways
@@ -41 +35 @@
 
 # write the items
-my $writer = new XML::Writer(DATA_MODE => 1, DATA_INDENT => 3);
+open(my $output, '>', $out_file) 
+    or die "Cannot open $outfile for writing, $!";
+
+my $writer = new XML::Writer(
+    DATA_MODE   => 1, 
+    DATA_INDENT => 3, 
+    OUTPUT      => $output,
+);
 
 $writer->startTag("items");
 for my $item (@items) {
-  $item->as_xml($writer);
+    $item->as_xml($writer);
 }
 $writer->endTag("items");
+
+close($output) or die "Cannot close $outfile, $!";
+exit;