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#!/usr/bin/perl
my $tag = uc(shift(@ARGV));
my $newLength = shift(@ARGV);
$tag =~ /G*(.*)/;
$tag2 = &translateIUPAC($1);
#print "$tag2\n";
while($line = <STDIN>){
chomp($line);
if($line =~ />(.*)/){
print "$line\n";
}
else{
$line =~ /$tag2(.*)/;
$parse = $1;
$truncate = substr($parse, 0, $newLength);
print "$truncate\n";
}
}
sub translateIUPAC()
{
my ($seq) = @_;
$seq=~s/W/\[AT\]/g;
$seq=~s/B/\[CGT\]/g;
$seq=~s/S/\[GC\]/g;
$seq=~s/N/\[ACTG\]/g;
$seq=~s/Y/\[CT\]/g;
$seq=~s/R/\[AG\]/g;
$seq=~s/D/\[AGT\]/g;
$seq=~s/H/\[ACT\]/g;
$seq=~s/M/\[AC\]/g;
$seq=~s/K/\[GT\]/g;
$seq=~s/V/\[ACG\]/g;
return $seq;
}
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