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#!/usr/bin/perl
# "Clean" a MS/DOS fasta file from weird characters that screw with e.g. Perl
my $usage = "cleanDOSfasta.pl inFile > outFile\n";
if(@ARGV != 1){
print $usage;
exit;
}
my $inFile = $ARGV[0];
open(IN, "<", $inFile) or die "Could not open file $inFile\n!";
LINE: while($line = <IN>){
next LINE if $line =~ m/^#/; #discard comments
$line =~ s/[\x0A\x0D]+//g; # remove all those ugly whitespaces
$line =~ s/(\n)(\r)//g; #remove them alllll!
print $line."\n";
}
close(IN) or die "Could not close file $inFile!\n";
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