--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/patho_typing.pl	Tue Jan 28 10:42:31 2020 -0500
@@ -0,0 +1,60 @@
+#!/usr/bin/env perl
+## A wrapper script to collect patho_typing.py output
+use strict;
+use warnings;
+use Cwd;
+use English;
+use File::Copy;
+use File::Basename;
+
+# Parse arguments
+my ($python) = @ARGV;
+
+# Run program
+runPathoTyping();
+collectOutput();
+exit 0;
+
+# Run patho_typing
+sub runPathoTyping {
+    my $abs_path = Cwd::abs_path($PROGRAM_NAME);
+    my $scriptdir = dirname($abs_path);
+    my $rematchdir = "$scriptdir/ReMatCh";
+    my $newpath = "PATH=$ENV{PATH}:$rematchdir";
+    `$newpath; $python`;
+     return 0;
+}
+
+sub collectOutput{
+    my $patho_type = "";
+    open(my $fh, '<', 'output_dir/rematch/rematchModule_report.txt') || die "Could not open file 'output_dir/rematch/rematchModule_report.txt' $!";
+    my @rematch_lines = <$fh>;
+    close($fh);
+    my @rematch_table = "";
+    my @rematch_total_table = "";
+    my $highest_coverage = 0;
+    foreach(@rematch_lines) {
+      if ($_ =~ m/\t/) { # Only table lines
+        my @elems = split('\t', $_);
+        if ($_ =~ m/#/) { # First line
+          s/_/ /g for @elems;
+          push(@rematch_table,join("\t", @elems[0,1,2,5]));
+          push(@rematch_total_table,join("\t", @elems[0,1,2,5]));
+        }
+        else {
+          push(@rematch_total_table,join("\t", @elems[0,1,2,5]));
+          if ($elems[1] > 90.0) { # Only genes with over 90% coverage in report table
+            push(@rematch_table,join("\t", @elems[0,1,2,5]));
+          }
+        }
+      }
+    }
+    open($fh, '>', 'pathotyper_rep_tab') || die "Could not open file 'pathotyper_rep_tab' $!";
+    print $fh @rematch_table;
+    close($fh);
+    open($fh, '>', 'pathotyper_rep_tot_tab') || die "Could not open file 'pathotyper_rep_tot_tab' $!";
+    print $fh @rematch_total_table;
+    close($fh);
+
+    return 0;
+}