Array of arrays in Perl

Question

I'm new to Perl, but I needed it to get some text out of some awful HTML file. In the code so far, I have got to the point I have extracted all the values I need (I verified it works with data dumper):

For every data record i.e. row of a 2D table they are called:

$org, $gene_name, $number, $motif_num, $pos, $strand, $seq

I have many data entries and each one would be a row, with the above values as the columns.

To do other stuff with them later, I want to make a 2D array structure, so I can loop through each entry (row) and pick out values I need and so on.

I thought the best way of doing this would to use the loop and for each data entry, after extracting the values with regexp matching, combine the values/columns into an array for the individual data record:

my @seidl_array_row = ($org, $gene_name, $number, $motif_num, $pos, $strand, $seq);

Then push this array onto the finished 2D array of arrays:

push @seidl_array, [ @seidl_array_row ];

(@seidl_array was defined with my before the loop.)

So in effect I get a 2D data table, where each element of the array @seidl_array is an array containing the values $org, $gene_name, $number, $motif_num, $pos, $strand, and $seq.

I'm new to Perl, so I don't know if this was the right way to do it programmatically, since I'm having issues when it comes to doing stuff later with this data. I wondered if the issue was with how I constructed the array of arrays in the first place. Examples in my book do it statically with simple data sets, and this is a much larger genomic data gtf file, so doing it statically is not really feasible.

What are the issues you are having later? For the record, your 2-dimensional array looks ok and secondly, you'll probably find it easier to extract data from HTML using an HTML-specific library, and not just regular expressions — matt freake
– matt freake, Commented Apr 15, 2013 at 12:26

Peter Mortensen · Accepted Answer · 2017-05-02 00:13:42Z

7

As far as I can see, there is nothing wrong with your approach. Using a reference to the array instead of copying the array, as choroba suggested, has the benefit that the data isn't copied unnecessarily (but remember: that only works if you declare @seidl_array_row inside the loop, otherwise you would just make several references to the same array).

You can have that same advantage by skipping the row array completely like so:

push @seidl_array, [ $org, $gene_name, $number, $motif_num, $pos, $strand, $seq ];

For some extra convenience in accessing the data, I often use arrays of hashes like so:

push @seidl_array, {
    org    => $org,
    name   => $gene_name,
    number => $number,
    motif  => $motif_num,
    pos    => $pos,
    strand => $strand,
    seq    => $seq,
};

This has the advantage that you don't have to remember the positions of the respective values in the array, but can access them by name.

edited May 2, 2017 at 0:13

Peter Mortensen

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answered Apr 15, 2013 at 12:36

tauli

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3 Comments

Jenny D Over a year ago

+1 for using hashes instead of arrays. It's a good habit to get into.

SJWard Over a year ago

Thanks, I've changed my code so as it uses a hash. So if I want to loop through all the elements then and do operations, is the correct way to go about it, say for example I want to print all the strand variables or otherwise work with them while (my %seidl_row = shift @seidl_array){ print Dumper $seidl_row{strand};}?

SJWard Over a year ago

I think I've come up with a loop like the above that works: for my $i (0 .. $#seidl_array){print "Finding locations of motifs per gene ", $seidl_array[$i]{geneID}, "\n";}

choroba · Accepted Answer · 2013-04-15 12:28:34Z

4

Your solution seems correct to me. Using [ @seidl_array_row ] creates a copy of the list, if you are correctly declaring the row with my inside the loop, you can store its reference directly to avoid unnecessary copying:

push @seidl_array, \@seidl_array_row;

answered Apr 15, 2013 at 12:28

choroba

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