Basic stub-out of reactome::chebi mapping script.

svn path=/; revision=57

diff --git a/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl b/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl
index 35a27335973dce232b96940e000df26d06cda029..ec89553b8ac647d95453e15fe8df0a49bf09dce2 100755 (executable)
--- a/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl
+++ b/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl
@@ -1,6 +1,37 @@
 #!/usr/bin/perl -w
 use strict;
 
-my $chebi_path = 
+# set paths to data files
+my $data_path = "/home/preecej/Documents/Projects/Reactome/";
+my $chebi_obo_file = "chebi_sample.obo";
+my $reactome_file = "RiceReferenceMolecules_sample.txt";
+my $mapped_output_file = "reactome_chebi_mapping.txt";
+
+# read files into arrays
+open(CHEBI_OBO_FILE,$data_path . $chebi_obo_file);
+my @chebi_obo_terms = <CHEBI_OBO_FILE>;
+chomp(@chebi_obo_terms);
+close CHEBI_OBO_FILE;
+
+open(REACTOME_FILE,$data_path . $reactome_file);
+my @reactome_ref_molecules = <REACTOME_FILE>;
+chomp(@reactome_ref_molecules);
+close REACTOME_FILE;
+
+# show arrays
+# print "$_\n" foreach @chebi_obo_terms;
+# print "$_\n" foreach @reactome_ref_molecules;
+
+# setup output file
+open(OUTPUT_FILE,">>" . $data_path . $mapped_output_file);
+
+#
+# do brute-force matching here
+#
+
+print OUTPUT_FILE "$_\n" foreach @reactome_ref_molecules;
+
+# cleanup
+close OUTPUT_FILE;
 
 exit;