imtakinbioinformatic has asked for the wisdom of the Perl Monks concerning the following question:

Hello, I'm trying to work on code that reads an input file that has lines that start with > then lines of characters (repeated many times). I want to put the line that starts with > into one array, and then put all of the lines following the >line into a separate array as one element (until the next > comes.) So I want to end up with one array that has all of those > lines as elements, and then another array that has all of the text behind each of those > lines as separate elements. My code is working for the > lines how I want, but I seem to just be filling the second array with the text that followed that first >. I feel like this is confusing, but any help would be greatly appreciated! 

 

foreach $line(@DNA){
if ($line=~/^>(\S+)/){
    $seqID=$1;
    push(@seqList, $seqID);
    push (@sequences,$dnaString);
}
    else{
        chomp $line;
        $dnaString=$dnaString .$line;}
}

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Re: Creating 2 arrays from a larger array
by tangent (Parson) on Mar 08, 2012 at 02:43 UTC
    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'
        );

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[d/l]
      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]
        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);

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[reply]
[d/l]
Re: Creating 2 arrays from a larger array
by Anonymous Monk on Mar 08, 2012 at 02:40 UTC
[reply]

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