--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/removeChar.pl	Fri Sep 17 19:29:45 2021 +0000
@@ -0,0 +1,57 @@
+#!/usr/bin/perl -w
+use strict;
+
+############################################################################
+# script to remove position or column from a multi-Fasta file
+# in function of a given character
+############################################################################
+
+
+my $inFile = $ARGV[0]; #'example_seq.fasta';
+my $char = $ARGV[1]; #'N';
+my @headers = ();
+my @sequences = ();
+my $index = 0;
+my $outFile = 'results.fna';
+open(IN,'<',$inFile) or die "Unable to read file $inFile: $!\n";
+while( defined( my $line = <IN> ) ){
+    chomp($line);
+    if( $line =~ m/^>/ ){
+        $headers[$index] = $line;
+        $index++;
+    }
+    else{
+        $sequences[$index-1] .= $line;
+    }
+}
+close(IN);
+my %lookup = ();
+for(my $i=0;$i<=$#sequences;$i++){
+    my $seq = $sequences[$i];
+    my $len = length($seq);
+        for(my $j=0;$j<$len;$j++){
+        my $residue = substr($seq,$j,1);
+        if( $residue eq $char ){
+            $lookup{$j} = 1;
+        }
+    }
+}
+#print "# Skipped the following positions (zero indexed):\n";
+#print "# ",join(", ", sort {$a <=> $b} keys (%lookup)), "\n";
+#print "# Cleaned sequences:\n";
+#open(OUT,'>',$outFile) or die "Unable to write file $outFile: $!\n";
+for(my $i=0;$i<=$#headers;$i++){
+    my $head = $headers[$i];
+    my $seq = $sequences[$i];
+    my $len = length($seq);
+    my $out = '';
+    for(my $j=0;$j<$len;$j++){
+        my $residue = substr($seq,$j,1);
+        $out .= $residue unless exists $lookup{$j};
+    }
+    print $head, "\n", $out, "\n";
+    #print OUT $head, "\n", $out, "\n";
+}
+#close(OUT);
+#print "\n";
+#print "End of program! Your result is written in file $outFile\n";