Re: Creating 2 arrays from a larger array

in reply to Creating 2 arrays from a larger array

Not sure of your data but this might help:

my @seqList;
my @sequences;
my $dnaString;
my $count = 0;

my @DNA = <DATA>;
foreach my $line (@DNA) {
    if ($line=~/^>(\S+)/){
        push (@seqList, $1);
        push (@sequences, $dnaString) if $count++;
        $dnaString = '';
    }
    else {
        chomp $line;
        $dnaString .= $line;
    }
}
push (@sequences, $dnaString); # need to push last one

__DATA__
>123 blah
abcdef
ghijkl
>456 de dah
mnopqr
>789 nothing wanted here
stuvwxyz


# OUTPUT
@seqList = (
          '123',
          '456',
          '789'
        );
@sequences = (
          'abcdefghijkl',
          'mnopqr',
          'stuvwxyz'
        );
[download]

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Re^2: Creating 2 arrays from a larger array by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 03:18 UTC
Thanks tangent! I'm confused how `push (@sequences, $dnaString)` ever operates. If the string matches >, it goes to the seqList array, so how is the @sequences array being created?	[reply] [d/l]
Re^3: Creating 2 arrays from a larger array by tangent (Parson) on Mar 08, 2012 at 03:32 UTC
You are in a loop, so $dnaString is being added to everytime the line doesn't match your start pattern. $dnaString is always one step behind @seqList so when you come to the next start line, it pushes the previous $dnaString onto @sequences, then clears it for the next iteration. Best thing to do is try it: set $count = 1 and see what happens. Update: after re-reading this I'm a bit confused myself. Better to put a print statement within the loop: `my $dnaString = ''; ... if ($line=~/^>(\S+)/){ print qq\|Count: $count, Match: $1, String: $dnaString\n\|; push (@seqList, $1);` [download]	[reply] [d/l]
Re^4: Creating 2 arrays from a larger array by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 04:08 UTC
uggg still not getting it. No errors but the elements I printed were all the same. I'll keep working, thanks for explaining!	[reply]
Re^5: Creating 2 arrays from a larger array by NetWallah (Canon) on Mar 08, 2012 at 06:15 UTC
Re^5: Creating 2 arrays from a larger array by tangent (Parson) on Mar 08, 2012 at 13:54 UTC
Re^5: Creating 2 arrays from a larger array by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 14:59 UTC
Re^4: Creating 2 arrays from a larger array by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 14:52 UTC
Yeah here's the file http://www.med.nyu.edu/rcr/rcr/course/smutans.fas	[reply]

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