Hi Vineet,
Since Perl provides strong feature of pattern matching of Regular
Expn you should use that.
Just read in the pattern GAGAGAGAGAAAAGA from the file and store it in a
scalar variable.
You can refer to the following perl code snippet for getting yout job done.
#! /usr/bin/perl
my $x = 'GAGAGAGAAAGG';
$x =~ s/G/GLY/g; # Search for pattern G globally and replace it with 'GLY'
$x =~ s/A/ALA/g; # Search for pattern A gloablly and replace it with 'ALA'
print $x; # Print replaced string
1. Read in the string from your file .
2. Search and replace the string as required
3. Write the string in another file
The code wont take more than 10-12 lines. And the beauty is you dont have to
iterate over your string.
Regards,
Suvajit
Vineet Pande wrote:
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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