Re: Comparing array of aligned sequences

Not being a bio guy, I don't understand your transfer function. However, when I run your code I get several Use of uninitialized value in string. Using Tip #4 from the Basic debugging checklist (Data::Dumper), I see some undef values in your array. Try to eliminate those first.

use Data::Dumper;
print Dumper(\@arr)
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Arrays in Perl start with index=0 by default, but you start filling the array at index=1. Maybe you want $seqcount++; at the end of your while loop?

If you just want your input file in an array-of-arrays (perldoc perdsc), this is simpler:

my @arr;
open (B, "temp.dat");
while (my $line=<B>) {
    chomp $line;
    $line =~ s/\s//g;
    my @temp = split //, $line;
    push @arr, [@temp];
}
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Re^2: Comparing array of aligned sequences by newtoperlprog (Sexton) on Jul 11, 2014 at 17:05 UTC
Thank you for your time and reply. I did some modifcations and now the program is printing 3 times each value on match. I guess I am not putting the print at the right place. #!/usr/bin/perl use warnings; use strict; use Data::Dumper; my $seqcount; my $pos; my $arrlen; my @arr = (); open (B, "temp.dat"); while (my $line=<B>) { chomp $line; $seqcount++; $line =~ s/\s//g; my @temp = split (//, $line); $arrlen = scalar(@temp); for ($pos=0;$pos<=$#temp;$pos++) { $arr[$seqcount][$pos] = $temp[$pos]; # print "$pos\t$arr[$seqcount][$pos]\n"; } } my $max_position = 0; $max_position = $arrlen if($arrlen > $max_position); for ($pos=0;$pos<=$max_position;$pos++) { for (my $s=1;$s<=$seqcount;$s++) { # print "$pos\t$s\t$arr[$s][$pos]\n"; if ($arr[$s][$pos] ne $arr[$seqcount][$pos]) { print "\n"; next; } else { print "$arr[$s][$pos]"; } } print "\n"; } [download] Do I need to push in another array after there is a match of values? Thanks for your help.	[reply] [d/l]

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Re^2: Comparing array of aligned sequences
by newtoperlprog (Sexton) on Jul 11, 2014 at 17:05 UTC

Thank you for your time and reply. I did some modifcations and now the program is printing 3 times each value on match. I guess I am not putting the print at the right place.

#!/usr/bin/perl
use warnings;
use strict;
use Data::Dumper;
my $seqcount; my $pos; my $arrlen;
my @arr = ();
open (B, "temp.dat");
while (my $line=<B>)
{
    chomp $line;
    $seqcount++;
    $line =~ s/\s//g;
    my @temp = split (//, $line);
    $arrlen = scalar(@temp);
    for ($pos=0;$pos<=$#temp;$pos++)
    {
        $arr[$seqcount][$pos] = $temp[$pos];
#        print "$pos\t$arr[$seqcount][$pos]\n";
    }
}

my $max_position = 0;
$max_position = $arrlen if($arrlen > $max_position);
for ($pos=0;$pos<=$max_position;$pos++)
{
    for (my $s=1;$s<=$seqcount;$s++)
    {
#        print "$pos\t$s\t$arr[$s][$pos]\n";
        
        if ($arr[$s][$pos] ne $arr[$seqcount][$pos])
        {
            print "\n";            
            next;
        }
        else
        {
            print "$arr[$s][$pos]";
    
        }
    } print "\n";
}
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