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diff snpEff/SnpEff.pl @ 23:a1ab979f4551 draft

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Uploaded
author dereeper
date Mon, 23 Mar 2015 05:52:17 -0400
parents 13cff72ec2d3
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/SnpEff.pl	Mon Mar 23 05:52:17 2015 -0400
@@ -0,0 +1,82 @@
+#!/usr/bin/perl
+
+use strict;
+use Getopt::Long;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <input VCF>
+    -o, --output        <output>
+    -g, --gff           <GFF annotation>
+    -f, --fasta         <Fasta of chromosomes>
+    -h, --html          <HTML output>
+~;
+$usage .= "\n";
+
+my ($input,$output,$gff,$fasta,$html);
+
+
+GetOptions(
+	"input=s"      => \$input,
+	"output=s"     => \$output,
+	"gff=s"        => \$gff,
+	"fasta=s"      => \$fasta,
+	"html=s"       => \$html
+);
+
+
+die $usage
+  if ( !$input || !$output || !$fasta || !$gff || !$html);
+
+
+if (!-e $gff){
+        die "Error: GFF input does not exist\n"
+}
+if (!-e $fasta){
+        die "Error: Fasta input does not exist\n"
+}
+
+#my $SNPEFF_PATH = "/usr/local/bioinfo/galaxy/galaxy_dist/tools/SNiPlay/SnpEff/snpEff";
+my $SNPEFF_PATH = $ENV{SNPEFF_JAR_PATH};
+
+
+my $session = $$;
+mkdir($session);
+mkdir("$session/data");
+mkdir("$session/data/genomes");
+mkdir("$session/data/myspecies");
+
+system("cp -rf $fasta $session/data/genomes/myspecies.fa");
+system("cp -rf $gff $session/data/myspecies/genes.gff");
+
+open(my $C,"$SNPEFF_PATH/snpEff.config");
+open(my $C2,">$session/snpEff.config");
+while(<$C>)
+{
+	if (/data_dir/)
+	{
+		print $C2 "data_dir = ./data\n";
+	}
+	elsif (/^genomes/)
+	{
+		print $C2 "genomes : \\n";
+        	print $C2 "myspecies, myspecies \\n";
+	}
+	else
+	{
+		print $C2 $_;
+	}
+}
+print $C2 "myspecies.genome : myspecies\n";
+close($C);
+close($C2);
+
+
+my $build_cmd = "java -jar $SNPEFF_PATH/snpEff.jar build -c $session/snpEff.config -gff3 myspecies";
+system($build_cmd);
+
+my $eff_cmd = "java -jar $SNPEFF_PATH/snpEff.jar eff -c $session/snpEff.config -o vcf -no-downstream -no-upstream myspecies -s $html $input >$output";
+system($eff_cmd);
+
+
+system("rm -rf $session");