Hi,
I need the wisdom of the monks for a problem.
I am trying to read a multi-sequence fasta file and then put each of the sequences in an array, after which I work on each array to get some measures.
I want to do all this within one program, so i tried using an array of arrays to capture all the sequences from one "> sequence header" to the next ">sequence header".
while (<INFILE>)
{
chomp;
push @dna,[split /^>(.*)/];
}
close INFILE;

[download]

The input is a file with a lot of fasta sequences like
>sequence header 1.
AAATATTATATATATTGCG
ATTATTATATGCGCGGCGC
>sequence header 2
AATTGGGCTCGCTGCTTTT
AGGAGGAGGAGCCCTCTCC
>sequence header 3
AATTGGCTGCTCGCTGCTC
AATGTGTCGGCGCGCGTGC

I want each of the sequences in an array, or atleast in an array, within an array of arrays.

I would appreciate any helpful suggestions.

Thanks

Kris

In reply to Splitting a multi-sequence fasta file into individual sequences in individual arrays by krish28

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