--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PGAP_wrapper2.pl	Thu Jun 24 13:51:52 2021 +0000
@@ -0,0 +1,65 @@
+#!/usr/bin/perl
+
+use strict;
+use Getopt::Long;
+use Bio::SeqIO;
+use File::Basename;
+my $dirname = dirname(__FILE__);
+use Cwd qw(cwd);
+my $dir = cwd;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+
+where <args> are:
+
+    -g, --genes          <list of gene fasta files. Comma separated list>
+    -p, --proteins       <list of protein fasta files. Comma separated list>
+    -o, --order          <list of samples in the same order. Comma separated list>
+    -o, --out            <output name>      
+~;
+$usage .= "\n";
+
+my ($genes,$proteins,$out,$order);
+
+GetOptions(
+"genes=s"        => \$genes,
+"proteins=s"     => \$proteins,
+"out=s"          => \$out,
+"order=s"        => \$order
+);
+
+
+die $usage
+  if ( !$proteins || !$genes || !$out || !$order);
+
+my @names = split(",",$order);
+my @list;
+mkdir("tmpdir$$");
+my @gene_files = split(/,/,$genes);
+my $n = 0;
+foreach my $gene_file(@gene_files){
+	my $particule = $names[$i];
+	system("cp $gene_file tmpdir$$/$particule.nuc");
+	$n++;
+}
+$n = 0;
+my @protein_files = split(/,/,$proteins);
+foreach my $protein_file(@protein_files){
+        my $particule = $names[0];
+	system("cp $protein_file tmpdir$$/$particule.pep");
+	open(F,"$protein_file");
+	open(F2,">tmpdir$$/$particule.function");
+	while(<F>){
+		if (/>(.*)/){
+			print F2 "$1	-	unknown\n";	
+		}
+	}
+	close(F);
+	close(F2);
+	$n++;
+}
+
+#chdir("$dirname/PGAP-1.2.1");
+my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@list)." --method GF";
+system($cmd);
+system("cp -rf outdir/1.Orthologs_Cluster.txt $out");