compare_masking.pl, merge_masking.pl : scripts to assess and merge th…

…e (soft-)masking for repeats that is produced by different pipelines, e.g. RepeatScout and CARP.

scripts/compare_masking.pl

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+#!/usr/bin/perl
+
+# Katharina J. Hoff
+# November 20th 2018
+
+
+use strict;
+use warnings;
+use Getopt::Long;
+
+my $usage = << 'ENDUSAGE';
+compare_masking	compare the repeat masking content of differently masked (same) assemblies
+
+SYNOPSIS
+
+compare_masking file1.fa file2.fa
+
+	file1.fa  softmasked fasta file
+	file2.fa  softmasked second fasta file
+
+OPTIONS
+
+    --help    output this help message
+
+WARNING: This script keeps two assemblies in memory, i.e. it is not suitable for large genomes!
+
+ENDUSAGE
+
+my ($help);
+
+GetOptions('help' => \$help);
+
+if($help){
+	print $usage;
+	exit(1);
+}
+
+
+my %masking1;
+my $key;
+open(FILE1, "<", $ARGV[0]) or die ("Could not open file $ARGV[0]!\n");
+	while(<FILE1>){
+		chomp;
+		if(m/^>/){
+			$masking1{$_} = "";
+			$key = $_;
+		}else{
+			$masking1{$key} .= $_;
+		}
+	}
+close(FILE1) or die ("Could not close file $ARGV[0]!\n");
+
+my %masking2;
+open(FILE2, "<", $ARGV[1]) or die ("Could not open file $ARGV[1]!\n");
+	while(<FILE2>){
+		chomp;
+		if(m/^>/){
+			$masking2{$_} = "";
+			$key = $_;
+		}else{
+			$masking2{$key} .= $_;
+		}
+	}
+close(FILE2) or die ("Could not close file $ARGV[1]!\n");
+
+
+my $only1 = 0;
+my $only2 = 0;
+my $both = 0;
+while( my($key, $value) = each(%masking1)){
+	my @arr1 = split(//, $value);
+	my @arr2 = split(//, $masking2{$key});
+	my $counter = 0;
+	foreach(@arr1){
+		if( ($_ =~ m/\p{Lowercase}/) and ($arr2[$counter] =~ m/\p{Lowercase}/)){
+			$both++;
+		}elsif($_ =~ m/\p{Lowercase}/){
+			$only1++;
+		}elsif($arr2[$counter] =~ m/\p{Lowercase}/){
+			$only2++;
+		}
+		$counter++;
+	}
+}
+
+print("Masked in both files: $both\n");
+print("Masked in File1, only: $only1\n");
+print("Masked in File2, only: $only2\n");

scripts/merge_masking.pl

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+#!/usr/bin/perl
+
+# Katharina J. Hoff
+# November 20th 2018
+
+use strict;
+use warnings;
+use Getopt::Long;
+
+my $usage = << 'ENDUSAGE';
+merge_masking.pl	take two softmasked (same) genome assemblies and mask all bases that are
+                    masked in one of the two files (softmasking).
+
+SYNOPSIS
+
+compare_masking file1.fa file2.fa
+
+	file1.fa  softmasked fasta file
+	file2.fa  softmasked second fasta file
+	file3.fa  output softmasked third fasta file
+
+OPTIONS
+
+    --help    output this help message
+
+WARNING: this script keeps two assemblies in memory, i.e. it is not suitable for large genomes!
+
+ENDUSAGE
+
+my ($help);
+
+GetOptions('help' => \$help);
+
+if($help){
+	print $usage;
+	exit(1);
+}
+
+
+my %masking1;
+my $key;
+open(FILE1, "<", $ARGV[0]) or die ("Could not open file $ARGV[0]!\n");
+	while(<FILE1>){
+		chomp;
+		if(m/^>/){
+			$masking1{$_} = "";
+			$key = $_;
+		}else{
+			$masking1{$key} .= $_;
+		}
+	}
+close(FILE1) or die ("Could not close file $ARGV[0]!\n");
+
+my %masking2;
+open(FILE2, "<", $ARGV[1]) or die ("Could not open file $ARGV[1]!\n");
+	while(<FILE2>){
+		chomp;
+		if(m/^>/){
+			$masking2{$_} = "";
+			$key = $_;
+		}else{
+			$masking2{$key} .= $_;
+		}
+	}
+close(FILE2) or die ("Could not close file $ARGV[1]!\n");
+
+
+open(FILE3, ">", $ARGV[2]) or die ("Could not open file $ARGV[2]!\n");
+while( my($key, $value) = each(%masking1)){
+	my @arr1 = split(//, $value);
+	my @arr2 = split(//, $masking2{$key});
+	my $counter = 0;
+	print(FILE3 $key."\n");
+	foreach(@arr1){
+		if( ($_ =~ m/\p{Lowercase}/) or ($arr2[$counter] =~ m/\p{Lowercase}/)){
+			print(FILE3 lc($_));
+		}else{
+			print(FILE3 $_);
+		}
+		$counter++;
+	}
+	print(FILE3 "\n");
+}
+close(FILE3) or die ("Could not close file $ARGV[2]!\n");