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Perl Program for Translation
#1
#!/usr/bin/perl -w
use strict;
my ($file,$line,$sequence,$i,$codon,$CODON,$protein);
my %genetic_code = qw(
TTT      F  
TCT      S
TAT      Y  
TGT      C  
TTC      F  
TCC      S  
TAC      Y 
TGC      C 
TTA      L  
TCA      S  
TAA      _  
TGA      _  
TTG      L  
TCG      S 
TAG      _  
TGG      W  
CTT      L  
CCT      P  
CAT      H  
CGT      R  
CTC      L  
CCC      P  
CAC      H 
CGC      R  
CTA      L  
CCA      P  
CAA      Q 
CGA      R  
CTG      L 
CCG      P  
CAG      Q  
CGG      R 
ATT      I  
ACT      T  
AAT      N  
AGT      S  
ATC      I  
ACC      T  
AAC      N  
AGC      S 
ATA      I  
ACA      T  
AAA      K 
AGA      R  
ATG      M  
ACG      T  
AAG      K  
AGG      R  
GTT      V  
GCT      A  
GAT      D   
GGT      G 
GTC      V  
GCC      A  
GAC      D   
GGC      G  
GTA      V  
GCA      A  
GAA      E  
GGA      G  
GTG      V  
GCG      A  
GAG      E   
GGG      G  
);

print "Enter the filename: ";
$file = <STDIN>;
chomp $file;
open (FILE, $file) or die "Cannot open file : $file \n\n";
# if there are 10 lines in the file then while loop iterates 10 times
# next command resets the while loop to the next line 
while ($line = <FILE>)
{
# Discard blank lines
if ($line =~ /^\s*#/ )
{ next; } 
# Discard comment line
elsif ($line=~/^#/)
{ next; }
# Discard fasta header line
elsif($line =~ /^>/ )
{ next; }
# Keep concatenating to $sequence string
else
{ $sequence .= $line; }
}
$sequence =~ s/\s//g ;
close FILE;

for ($i=0; $i < (length ($sequence) - 2) ; $i += 3)
{
# From the string '$sequence' at position '$i' extract 3 characters & store it in '$codon'
$codon = (substr($sequence,$i,3));
# Converting any lower case characters to upper case
$CODON = uc $codon;
# Checking for the existence of CODON in the hash %genetic_code
if(exists $genetic_code{$CODON})
# The corresponding amino acid in the hash is stored in $protein
{ $protein .= $genetic_code{$CODON}; }
else
{ die "Bad codon !! \n\n";}
}

print "The translated protein sequence is : $protein \n\n";
  

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Perl Program for Translation00