Hello! I am trying to write a script that detects SNPs and their position in DNA sequences. Simply put, A SNP is when there is a change in A, T, C, or G between sequences, therefore...

A could change to T, C, to G

T could change to C, G, or A

G could change to C, T or A

C could change to G, T or A

For Example:

Sequence 1: ATGGAT

Sequence 2: ACGGAG

There are 2 SNPs here.

SNP 1 is the T --> C is position 2 of the sequence. SNP 2 is the T -->G in position 6 of the sequence.

Criteria for the script:

Only 2 sequences can be entered on the command line The 2 sequences must be equal length Find the SNP and the position of the SNP (starting from position 1 not 0) Print out data- for example using the sample above

Pos 2: T => C

Pos 6: T =>G

Found 2 SNPs.

This is what I have so far, but I am not sure how to proceed... 

 
#!/usr/bin/env perl 
# file: 08-snps.pl
use strict;
use warnings;
use autodie;

my $number_seqs = scalar @ARGV;

if($number_seqs != 2){
  print "Please provide two sequences \n";
}
for (my $i=0; $i<$number_seqs; $i++){
    if(length($ARGV[$i]) != length($ARGV[0])){
        print "Please ensure the sequences are the same length \n";
    }
}


 
my $var =  $ARGV[0];
print $var,"\n";

my $var2 = my $var[0];
print $var2,"\n";

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In reply to Help tracking changes in array by reebee3

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