Create ALLHiC2ALLMAPS.pl

Huyuxi08 · Jun 28, 2019 · 3d49400 · 3d49400
1 parent 26a0395
commit 3d49400
Showing 1 changed file with 23 additions and 0 deletions.
diff --git a/scripts/ALLHiC2ALLMAPS.pl b/scripts/ALLHiC2ALLMAPS.pl
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+#!/usr/bin/perl -w
+### Convert ALLHiC output AGP file to ALLMAPS input csv file
+print "Convert ALLHiC output AGP file to ALLMAPS input csv file\n";
+die "Usage: perl $0 groups.agp\n" if(!defined $ARGV[0]);
+
+my $agp = $ARGV[0];
+open(OUT, "> hic.csv") or die"";
+print OUT "Scafffold ID,scaffold position,LG,genetic position\n";
+open(IN, "grep -v 'contig' $agp|") or die"";
+while(<IN>){
+	chomp;
+	my @data = split(/\s+/,$_);
+	if($data[8] eq "+"){
+		$a = $data[6]; $b = $data[7];
+	}elsif($data[8] eq "-"){
+		$a = $data[7]; $b = $data[6];
+		}
+	print OUT "$data[5],$a,$data[0],$data[1]\n";
+	print OUT "$data[5],$b,$data[0],$data[2]\n";
+	}
+close IN;
+close OUT;
+