# HG changeset patch
# User dereeper
# Date 1624557382 0
# Node ID d8c5bea1cce2cd7ad47c0e939ca252ee44d85573
# Parent  70b7a5270968937c2188bdb359f7e8e3a683a5da
Uploaded

diff -r 70b7a5270968 -r d8c5bea1cce2 PGAP-1.2.1/PGAP.pl
--- a/PGAP-1.2.1/PGAP.pl	Thu Jun 24 16:15:34 2021 +0000
+++ b/PGAP-1.2.1/PGAP.pl	Thu Jun 24 17:56:22 2021 +0000
@@ -1804,7 +1804,8 @@
 		system("grep '>' All.pep > genelist");
 		system("$formatdb -p T -i All.pep");
 		system("$blastall -p blastp -i All.pep -d All.pep -M BLOSUM45 -m9 -e $evalue -o All.blastp -a $thread");
-		system("perl ./Blast_Filter.pl All.blastp All.pep $coverage $identity $score | $mcl - --abc -I 2.0 -o All.cluster");
+		my $dircur = dirname(__FILE__);
+		system("perl $dircur/Blast_Filter.pl All.blastp All.pep $coverage $identity $score | $mcl - --abc -I 2.0 -o All.cluster");
 		&FormatCluster("All.cluster","genelist",$spnum,\@clusters);
 		#system("rm -rf *.pep* All.blastp All.cluster genelist");
 	}
diff -r 70b7a5270968 -r d8c5bea1cce2 PGAP.xml
--- a/PGAP.xml	Thu Jun 24 16:15:34 2021 +0000
+++ b/PGAP.xml	Thu Jun 24 17:56:22 2021 +0000
@@ -6,7 +6,6 @@
 	 <requirement type="package" version="14.137">mcl</requirement>
 	 <requirement type="package" version="3.697">phylip</requirement>
 	 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
-	 <requirement type="package" version="0.07">perl-statistics-linefit</requirement>
 </requirements> -->
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 70b7a5270968 -r d8c5bea1cce2 PGAP_wrapper2.pl
--- a/PGAP_wrapper2.pl	Thu Jun 24 16:15:34 2021 +0000
+++ b/PGAP_wrapper2.pl	Thu Jun 24 17:56:22 2021 +0000
@@ -32,8 +32,10 @@
 die $usage
   if ( !$proteins || !$genes || !$out || !$order);
 
+if ($order =~/^,(.*)$/){
+	$order = $1;
+}
 my @names = split(",",$order);
-my @list;
 mkdir("tmpdir$$");
 my @gene_files = split(/,/,$genes);
 my $n = 0;
@@ -45,7 +47,7 @@
 $n = 0;
 my @protein_files = split(/,/,$proteins);
 foreach my $protein_file(@protein_files){
-        my $particule = $names[0];
+        my $particule = $names[$n];
 	system("cp $protein_file tmpdir$$/$particule.pep");
 	open(F,"$protein_file");
 	open(F2,">tmpdir$$/$particule.function");
@@ -60,6 +62,6 @@
 }
 
 #chdir("$dirname/PGAP-1.2.1");
-my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@list)." --method GF";
+my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@names)." --method GF";
 system($cmd);
 system("cp -rf outdir/1.Orthologs_Cluster.txt $out");