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Hashes, Bioinformatics, Counting Codons

anzdro
New User

Apr 13, 2013, 11:06 AM

Post #1 of 4 (969 views)

Hashes, Bioinformatics, Counting Codons	Can't Post

Hi,
I'm just starting out with bioinformatics while using Perl. There's a certain problem I've been having in getting the data I want. There is a list of codons and it's my job to go through it and count how many times each specific codon observed throughout the data and print out the name of the codon and the number of times it was seen. I've written the following code:

while (<>) {
@codon = split;
%hash = @codon;
}
foreach $key (keys %hash) {
$tallyscore{$key}++;
print "$key $tally{$key}\n";
}

The code gives me the codon names that I want but does not give the numbers that I'm looking for. I'm just starting out with perl and any help would be greatly appreciated!

FishMonger
Veteran / Moderator

Apr 13, 2013, 11:20 AM

Post #2 of 4 (966 views)

Re: [anzdro] Hashes, Bioinformatics, Counting Codons [In reply to]	Can't Post

Please post some sample lines of your data and what output you expect from that sample.

g4143
Novice

Apr 13, 2013, 11:20 AM

Post #3 of 4 (965 views)

Re: [anzdro] Hashes, Bioinformatics, Counting Codons [In reply to]	Can't Post

Try something like below.

Code

#!/usr/bin/perl 
 
use warnings; 
use strict; 
 
my @codon; 
my %hash; 
 
while ( <> ) 
{ 
	@codon = split; 
	++$hash{$_} foreach(@codon); 
} 
 
foreach(sort(keys(%hash))) 
{ 
	print "$_ has a value->$hash{$_}\n"; 
}

anzdro
New User

Apr 13, 2013, 11:46 AM

Post #4 of 4 (955 views)

Re: [g4143] Hashes, Bioinformatics, Counting Codons [In reply to]	Can't Post

Wow, thank you! This really helped!

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