Open Reading Frame program not printing Amino Acid Sequences - macos

Question

I am working on a program that will be able to read a gene sequence and give me the Open Reading Frames (ORF) and then the protein sequence of each ORF. I have already gotten the code to work for finding the ORFs- but no amino acids will print. I am using Perl on my Mac.
I would like to get the code to tell me the string of amino acids produced from the open reading frames.
Here is my code:
#!/usr/bin/perl
#ORF_Find.txt -> finds long orfs in a DNA sequence
open(CHROM, "chr03.txt"); #Open file chr03.txt containing yeastchrom. 3
$DNA = ""; #start with empty DNA sequence
$header = <CHROM>; #get header of sequence
#Read line from file, join to end of $DNA, repeat until end of file
while ($current_line = <CHROM>)
{
chomp($current_line); #remove newline from end of current_line
$DNA= $DNA . $current_line;
}
#length of DNA sequence
$DNA_length = length($DNA);
#flag for ORF finder
$inORF=0;
#number of ORFs found
$numORFs = 0;
#minimum length
$minimum_codons =100;
#search each reading frame
for ($frame =0; $frame<3; $frame++)
{
print "\nFinding ORFs in frame: +" . ($frame + 1) . "\n";
#search for sequence match and print position of match if found
for ($i =frame; $i<=($DNA_length-3);$i += 3)
{
#get current codon from sequence
$codon= substr ($DNA, $i, 3);
#if not in orf search for ATG, else search for stop codon
if ($inORF == 0)
{
#if current codon is ATG, start ORF
if ($codon eq "ATG")
{
$inORF = 1;
$ORF_length = 1;
$ORF_start = $i;
}
}
elsif($inORF ==1)
{
#if current codon is a stop codon, end ORF
if ($codon eq "TGA" || $codon eq "TAG" || $codon eq "TAA")
{
#if ORF has at least min number of codons,print location
if ($ORF_length >= $minimum_codons)
{
print "FOUND ORF AT POSITION $ORF_start,";
print "length = $ORF_length\n";
$numORFs++;
}
#reset ORF variables
$inORF = 0;
$ORF_length = 0;
}
else
{
#increase length of ORF by one codon
$ORF_length++;
}
}
}
}
#change T to U
$DNA =~ s/T/U/g;
#search each ORF
for ($i=$ORF_start; $i<=($ORF_length-3); $i+=3)
{
#get codon from each ORF
$aa_codon= substr($DNA, $i, 3);
#find amino acids
foreach ($aa_codon eq "ATG")
{
print ("M") #METHIONINE
}
foreach ($aa_codon =~/UU[UC]/)
{
print ("F") #PHENYLALANINE
}
foreach ($aa_codon =~/UU[AG]/ || $aa_codon=~/CU[UCAG]/)
{
print ("L"); #LEUCINE
}
foreach ($aa_codon =~/AU[UAC]/)
{
print ("I"); #ISOLEUCINE
}
foreach ($aa_codon =~/GU[UACG]/)
{
print ("V"); #VALINE
}
foreach ($aa_codon =~/UC[UCAG]/ || $aa_codon=~/AG[UC]/)
{
print ("S"); #SERINE
}
foreach ($aa_codon =~/CC[UCAG]/)
{
print ("P"); #PROLINE
}
foreach ($aa_codon =~/AC[UCAG]/)
{
print ("T"); #THREONINE
}
foreach ($aa_codon =~/GC[UCAG]/)
{
print ("A"); #ALANINE
}
foreach ($aa_codon =~/UA[UC]/)
{
print ("Y"); #TYROSINE
}
foreach ($aa_codon =~/CA[UC]/)
{
print ("H"); #HISTIDINE
}
foreach ($aa_codon =~/CA[AG]/)
{
print ("G"); #GLUTAMINE
}
foreach ($aa_codon =~/AA[UC]/)
{
print ("N"); #ASPARAGINE
}
foreach ($aa_codon =~/AA[AG]/)
{
print ("K"); #LYSINE
}
foreach ($aa_codon =~/GA[UC]/)
{
print ("D"); #ASPARTIC ACID
}
foreach ($aa_codon =~/GA[AG]/)
{
print ("E"); #GLUTAMIC ACID
}
foreach ($aa_codon =~/UG[UC]/)
{
print ("C"); #CYSTINE
}
foreach ($aa_codon eq "UGG")
{
print ("W"); #TRYPTOPHAN
}
foreach ($aa_codon =~/AG[AG]/ || $aa_codon =~/CG[UCAG]/)
{
print ("R"); #ARGININE
}
foreach ($aa_codon =~/GG[UCAG]/)
{
print ("G"); #GLYCINE
}
foreach ($aa_codon =~/UA[AG]/|| $aa_codon eq "UGA")
{
print ("*") #STOP
}
}
#if no ORFS found, print message
if ($numORFs ==0)
{
print ("NO ORFS FOUND\n");
}
else
{
print ("\n$num_ORFs ORFS WERE FOUND\n");
}

Answer 1

First, this question would probably be more appropriate for a forum such as seqAnswers or BioStars. That aside, writing your own 6-frame translation script is a complex task, especially if you want to account for IUPAC ambiguous nucleotides. There are already lots of scripts and tools out there that do this. Probably the easiest suggestion I can make is to use one of the existing tools. Try mine, for example:
https://github.com/hepcat72/sixFrameTranslation/archive/master.zip
My script wasn't public until just now. I have opened it up so that you can use it. Just run it to get a usage.
Other than that, if you want to get your version running properly, the first thing you can do is change your she-bang to:
#!/usr/bin/perl -w
Note the -w. Then, add this line to the top of your script:
use strict;
It will help you debug issues such as the missing dollar sign in one of your for loops:
for ($i =frame; $i<=($DNA_length-3);$i += 3)
It should be:
for ($i =$frame; $i<=($DNA_length-3);$i += 3)
And BTW, it doesn't matter that you're running perl on your Mac. It's just perl. "Mac perl" was a project to create a perl environment back in the pre-OS-X days.