Dear Perl Guru:
I want to write a script which takes input a text file with sequence of
alphabets (amino acids) like GAGAGAGAGAAAAGA etc. and converts them to a
three letter corresponding code [G= GLY, A= ALA]. The output should be then
written to another file. I wrote the following script, but it seems it goes
in an infinite loop and only prints GLY GLY GLY....infinitely for an input
of GAAAGAGAAGA etc. Any suggestions? Thanks in advance
-Vineet
****************************************
#!/usr/bin/perl
use warnings;
my $fasta_file = "fasta.txt"; #this contains single letter code#
chomp $fasta_file;
my $charmm_file = "charmm.txt"; #this is expected to have three letter
converted#
unless (open (IN, $fasta_file) )
{
print "Cannot open file \"fasta_file\"\n\n";
exit;
}
open OUT, ">$charmm_file" or die;
@protein = <IN>;
close IN;
$protein = join( '', @protein);
$protein =~ s/\s//g;
for ( $position=0; $position < length $protein; ++$protein )
{
$aa = substr($protein, $position, 1);
if ($aa eq 'G') {
$praa = "GLY ";
print OUT $praa;
}
elsif ($aa eq 'A') {
$prab = "ALA ";
print OUT $prab;
}
else {
exit;
}
}
close OUT;
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