diff HaplophyleInBatch.pl @ 0:6f11162b6fa2 draft

planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/HaplophyleInBatch.pl	Tue Aug 14 08:04:23 2018 -0400
@@ -0,0 +1,107 @@
+#!/usr/bin/perl
+
+use strict;
+use Switch;
+use Getopt::Long;
+use Bio::SeqIO;
+
+my $HAPLOPHYLE_EXE = "java -Xmx2048m -jar /usr/local/bioinfo/sniplay/Haplophyle/NetworkCreator_fat.jar";
+my $NEATO_EXE = "neato";
+my $CONVERT_EXE = "convert";
+my $RSCRIPT_EXE = "/usr/local/bioinfo/R/default/bin/Rscript";
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <input>
+<opts>
+    -r, --rscript       <R scripts in zipfile>
+~;
+$usage .= "\n";
+
+my ($infile,$r_zip);
+
+
+GetOptions(
+	"input=s"    => \$infile,
+	"rscript=s"  => \$r_zip
+);
+
+
+die $usage
+  if ( !$infile);
+
+
+if (-e $r_zip)
+{
+	system("unzip $r_zip");
+}
+  
+my %inputs;
+my $gene;
+my $data = "";
+open(my $I,$infile);
+while(<$I>) 
+{
+	if (/===(.*)===/)
+	{
+		$gene = $1;
+	}
+	else
+	{
+		$inputs{$gene}.= $_;
+	}
+}
+close($I);
+
+
+foreach my $gene(keys(%inputs))
+{
+	open(F,">$gene.distinct_haplo.fas");
+	print F $inputs{$gene};
+	close(F);
+	
+	my $input   = "$gene.distinct_haplo.fas";
+    my $outfile = "$gene.network.dot";
+    my $out_png = "$gene.network.png";
+
+	my $command = "$HAPLOPHYLE_EXE -in $input -out $outfile >> $gene.haplophyle.log 2>&1";
+	system($command);
+
+	
+
+	
+	open(OUTFILE,"$outfile");
+	open(OUTFILE2,">$outfile.vis");
+	print OUTFILE2 "var nodes = [\n";
+	open(INFILE,"$input");
+	while(<INFILE>)
+	{
+		if (/>haplo(\d+)\|(\d+)/)
+		{
+			print OUTFILE2 "{id: $1, label: 'Haplo$1',shape:'image',radius:'$2'}\n";
+		}
+	}
+	close(INFILE);
+	print OUTFILE2 "];\n";
+	print OUTFILE2 "var edges = [\n";
+	my $n = 0;
+	while(<OUTFILE>)
+	{
+		my $line = $_;
+		if (/^haplo(\d+) -- haplo(\d+)/)
+		{
+			my $from = $1;
+			my $to = $2;
+			
+			print OUTFILE2 "{from: $from, to: $to,length:'7',style: 'line',color:'black',},\n";
+		}	
+
+	}
+	close(OUTFILE);
+	print OUTFILE2 "];\n";
+	close(OUTFILE2);
+}
+
+system("zip networks.zip *network.dot");
+#system("zip pies.zip *pie.eps");
+