HI Shlomi,
Thanks for your comments about best practise which I have implemented, Any
ideas on why my hash of arrays of arrays is misbehaving?
Thanks
Nat
On 1 Jul 2015, at 15:42, Shlomi Fish <shlo...@shlomifish.org> wrote:
> 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
>
>
> --
> -----------------------------------------------------------------
> Shlomi Fish http://www.shlomifish.org/
> List of Text Editors and IDEs - http://shlom.in/IDEs
>
> Chuck Norris can read Perl code that was RSA encrypted.
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