Hi Nat,
some comments about your code.
On Wed, 1 Jul 2015 13:00:53 +0100
nco...@ebi.ac.uk wrote:
> Hi,
> I need some help with a hash of array of array.
> this is my input data structure:
> gene a al1 data1 data2 data9
> gene b al2 data3 data4 data10
> gene b al3 data5 data6 data12
> gene b al4 data7 data8 data12
>
> I take each data variable, see above, from a sql query and parse the data
> to build a new data structure: a hash of arrays of arrays.
> In the input data presented here, the first column will be the key of the
> hash and the other 4 columns should compose 4 arrays.
> example :Each gene (gene a gene b ..) should be the keys, the al column
> should be the first array, data1,3,5,7 should be in the second array and
> so on for the third and fourth array. further more the data in the arrays
> should be unique. Data should be grouped depending on their keys, I am
> expecting this structure below, furthermore each variable in an array
> should be unique. ex: for gene b key in the 4th array data12 should appear
> once.
>
> Thanks for any tips.
> Nat
>
> this is what I would like to achieve (dataDumper format)
>
> $VAR1 = {
> gene b => [
Note that you need to quote the hash key if it contains whitespace:
'gene b' => [
> [
> 'al4','al2','al3'
> ],
> [
> 'data7','data3','data5'
> ],
> [
> 'data8','data4','data6'
> ],
> [
> 'data12','data10'
> ]
> ],
>
> gene a => [
> ['al1'],
> ['data1'],
> ['data2'],
> ['data9']
> ]
> };
>
>
> using the script below and the data dumper, I create a structure which is
> not correct some of the data is erased and other grouped wrongly, 'gene a'
> data goes into 'gene b' . gene a is empty.
>
> $VAR1 = {
> gene b => [
> [
> 'al1',
> 'al2',
> 'al3'
> ],
> [
> 'data1',
> 'data3',
> 'data5'
> ],
> [
> 'data2',
> 'data4',
> 'data6'
> ],
> [
> 'data9',
> 'data10',
> 'data12'
> ]
> ],
> gene a => [
> [],
> [],
> [],
> []
> ]
> };
>
>
>
> here is my code
>
> #!/usr/local/bin/perl
> use strict;
> use warnings;
It's good that you are using strict and warnings.
> use DBI;
> use Data::Dumper;
> use List::MoreUtils qw(uniq);
>
>
>
> my $subrow_hash;
> my $row_hash;
> my %hasharray;
You should not predeclare your variables:
http://perl-begin.org/tutorials/bad-elements/#declaring_all_vars_at_top
>
>
> my $geno_dbh = DBI->connect( credential...} ) || die "Database
> connection not made: $DBI::errstr";
> print STDERR "Connection...\n";
>
>
> my $subsql = "SELECT * FROM table_2015";
> #this is the table structure
> #gene a al1 data1 data2 data9
> #gene b al2 data3 data4 data10
> #gene b al3 data5 data6 data12
> #gene b al4 data7 data8 data12
>
In general "SELECT *" is not recommended and you should list your fields
explicitly.
>
> my $subresult = $geno_dbh->prepare($subsql);
> $subresult->execute() or die "SQL Error: $DBI::errstr\n";
>
> my @gene_name_list;
> my @allele_list;
> my @mp_list;
> my @mp_list_def;
> my @unique_mp_def;
> my $Xref;
> my @unique_gene_name_list ; # unique gene only
> my @unique_allele_list;# unique allele only
> my @unique_mp_list;# unique MP terms only
> my $list;
More predeclarations.
> while ( $subrow_hash = $subresult->fetchrow_hashref) {
>
Better have a "my $subrow_hash" here.
> my $symbol_id=$subrow_hash->{symbol};#this is the first set of data
> for the first array
1. The line is too long.
2. There are no spaces around the equal sign "=".
3. Perhaps make it an array.
>
> my $allele_id=$subrow_hash->{allele_symbol};#this is the 2nd set of
> data for the 2nd array
>
> my $mp_id=$subrow_hash->{phenotype_acc};#this is the 3rd set of data
> for the 3rd array
>
> my $mp_def=$subrow_hash->{name};#this is the fourth set of data for
> the fourth array
>
> $Xref=$subrow_hash->{xref_acc}; #this is the key of the hash (gene a
> and gene b)
>
>
> $list=[[@gene_name_list], [@allele_list], [@mp_list],
> [@mp_list_def]];#create arrays of arrays
>
$list here accumulates several lists.
> if ($Xref){
>
>
> $hasharray{$Xref} = $list; #create a hash of arrays of arrays
> for a specific key
> @gene_name_list =@{$list->[0]}; #maybe not necessary to
> declare this. @allele_list =@{$list->[1]};
> @mp_list =@{$list->[2]};
> @mp_list_def =@{$list->[3]};
>
Why is the assignment to the arrays again necessary.
>
>
> if ($symbol_id){
It's better to use defined here:
http://perldoc.perl.org/functions/defined.html
> push (@gene_name_list, $symbol_id); #fill arrays with data
> }
> if ($allele_id){
> push (@allele_list, $allele_id);
> }
> if ($mp_id){
> push (@mp_list, $mp_id);
> }
> if ($mp_def){
> push (@mp_list_def, $mp_def);
> }
> }
>
>
Perhaps you wish to peruse the resources in:
http://perl-begin.org/topics/references/
Regards,
Shlomi Fish
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