Hi Monks! Here's what my data looks like: 
File#1
dna:
species_1  ACCATGATACGATG
species_2  GGTTTCGACGCAGA
species_3  GGACTCAGCGACTA

File#2
morph:
species_1  001001010201001001
species_2  002010200210120201
species_4  001001110000000101
species_5  111001001001000201

[download]
If both data types exist for a species, I would like to append the morph data to the dna data. If a species is missing one of the data types, I would like to append as many "?"s as there are elements in the missing data partition: 
species_1  ACCATGATACGATG001001010201001001
species_2  GGTTTCGACGCAGA002010200210120201
species_3  GGACTCAGCGACTA??????????????????
species_4  ??????????????001001110000000101
species_5  ??????????????111001001001000201

[download]
I am completely new to Perl. What is the best strategy here? I tried constructing an hash of anonymous array refs: 
open IN, "dnamorph.txt" or die $!;
my %data;
my $taxon;
while (<IN>) {
    if (/(^\w+)(\t+)(\w+)/) {
        $taxon = $1;
        push @{ $data{$taxon} }, $3;
    }
}

[download]
Here, I couldn't figure out how to recognize if one of the partitions is missing and fill it with "?"s. My hash of de-refed arrays looked like this: 
species_1  ACCATGATACGATG001001010201001001
species_2  GGTTTCGACGCAGA002010200210120201
species_3  GGACTCAGCGACTA
species_4  001001110000000101
species_5  111001001001000201

[download]
I also tried to make a hash of hashes for each data partition, eg: 
open DNAA, "dna.nxs" or die $!;
my %ddata;
while (<DNAA>) {
    if (/(^\w+)(\t+)(\w+)/) {
        $ddata{ $1} = {
            dna => $3,
        };
    }
}

[download]
My data looks likes this: 
species_six: dna=TTGGGACAGCCGAGGCACGA 
species_two: dna=AAAATCGGGCGGCGCTTTTC 
species_five: dna=TTCCAGGACATCGGCATACG 
species_three: dna=GGGGCCCCAATATCGATACG 
species_four: dna=GGGGAGGACGTAGATATTAT 
species_one: dna=ACTGTTTCGTAGGGCTAGGA 

species_two: morph=111101011011011 
species_five: morph=111101011011011 
species_three: morph=012111011011011 
species_four: morph=112111011011011 
species_one: morph=110111011011111

[download]
Here, I can't figure out how to combine the 2 hashes of hashrefs without clobbering some values. Any help would be much apreciated, erio

In reply to Combining hashes of hahses? by erio

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