Hello all,

I am sure you would have heard this all before but I shall say it again. I am a new user of perl and would like help defining my hash. I have an input text file containing 11 columns of information that I have initialized. A snippet of the file and my code are shown below. 

File:
ID    Symbol    Taxon    Taxon Name    Evidence    GO ID    GO Name   
+ Aspect    Reference    With    Source
H1SXX9    Symbol1    12345    Homo Sapiens    IEA    GO:0015031    pro
+tein transport    Process    GO_REF:0000002    InterPro:IPR027282    
+InterPro
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0003824    cat
+alytic activity    Function    GO_REF:0000002    InterPro:IPR003607  
+  InterPro
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0008152    met
+abolic process    Process    GO_REF:0000002    InterPro:IPR002912    
+InterPro
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0008728    GTP
+ diphosphokinase activity    Function    GO_REF:0000003    EC:2.7.6.5
+    UniProt
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0015969    gua
+nosine tetraphosphate metabolic process    Process    GO_REF:0000002 
+   InterPro:IPR004811|InterPro:IPR007685    InterPro
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0016301    kin
+ase activity    Function    GO_REF:0000038    UniProtKB-KW:KW-0418   
+ UniProt
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0016310    pho
+sphorylation    Process    GO_REF:0000038    UniProtKB-KW:KW-0418    
+UniProt
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0016597    ami
+no acid binding    Function    GO_REF:0000002    InterPro:IPR002912  
+  InterPro
H1SXZ5    Symbol2    12345    Homo Sapiens    IEA    GO:0016740    tra
+nsferase activity    Function    GO_REF:0000038    UniProtKB-KW:KW-08
+08    UniProt
H1SXZ8    Symbol3    12345    Homo Sapiens    IEA    GO:0006812    cat
+ion transport    Process    GO_REF:0000002    InterPro:IPR002524    I
+nterPro
H1SXZ8    Symbol3    12345    Homo Sapiens    IEA    GO:0008324    cat
+ion transmembrane transporter activity    Function    GO_REF:0000002 
+   InterPro:IPR002524    InterPro
H1SXZ8    Symbol3    12345    Homo Sapiens    IEA    GO:0030001    met
+al ion transport    Process    GO_REF:0000002    InterPro:IPR006121  
+  InterPro
H1SXZ8    Symbol3    12345    Homo Sapiens    IEA    GO:0046872    met
+al ion binding    Function    GO_REF:0000002    InterPro:IPR006121   
+ InterPro
H1SXZ8    Symbol3    12345    Homo Sapiens    IEA    GO:0055085    tra
+nsmembrane transport    Process    GO_REF:0000002    InterPro:IPR0025
+24    InterPro
H1SY02    Symbol4    12345    Homo Sapiens    IEA    GO:0006810    tra
+nsport    Process    GO_REF:0000002    InterPro:IPR002898    InterPro
H1SY02    Symbol4    12345    Homo Sapiens    IEA    GO:0006810    tra
+nsport    Process    GO_REF:0000038    UniProtKB-KW:KW-0813    UniPro
+t
H1SY02    Symbol4    12345    Homo Sapiens    IEA    GO:0008565    pro
+tein transporter activity    Function    GO_REF:0000002    InterPro:I
+PR002898    InterPro
H1SY02    Symbol4    12345    Homo Sapiens    IEA    GO:0015031    pro
+tein transport    Process    GO_REF:0000038    UniProtKB-KW:KW-0653  
+  UniProt
H1SY06    Symbol5    12345    Homo Sapiens    IEA    GO:0004129    cyt
+ochrome-c oxidase activity    Function    GO_REF:0000002    InterPro:
+IPR000883|InterPro:IPR004677|InterPro:IPR023615|InterPro:IPR023616   
+ InterPro
H1SY06    Symbol5    12345    Homo Sapiens    IEA    GO:0004129    cyt
+ochrome-c oxidase activity    Function    GO_REF:0000003    EC:1.9.3.
+1    UniProt
H1SY06    Symbol5    12345    Homo Sapiens    IEA    GO:0005506    iro
+n ion binding    Function    GO_REF:0000002    InterPro:IPR000883    
+InterPro

[download]
Code:
open(IN,$annotationfile) or die "Can't open $annotationfile\n";
while(<IN>){
    chomp;
    @data = split(/\t/,$_);
    $Column1 = @data[0];
    $Column2 = @data[1];
    $Column3 = @data[2];
    $Column4 = @data[3];
    $Column5 = @data[4];
    $Column6 = @data[5];
    $Column7 = @data[6];
    $Column8 = @data[7];
    $Column9 = @data[8];
    $Column10 = @data[9];
    $Column11 = @data[10];
print "$Column1\t$Column2....\t$Column11\n";

foreach $_ (1..$#data){
$GOHash{"$Symbols"}{"$GO_Names"} = "$IDs";
foreach $Symbols (@data) {
foreach my $name (sort {$a <=> $b} (keys %GOHash) ) {
    foreach my $annotation (keys %{ $GOHash{$name} }) {
    print "$name, $annotation: $GOHash{$name}{$annotation}\n";
close(IN);
}
}
}
}
}

[download]

I know that my columns are initialized because I see the correct information when I print. I am experiencing problems creating a multidimensional hash. Sorry that the syntax is not correct, I did it for simplicities sake,however this is what I would like to hash: % hash1 = Column1 => Column 2. %hash2 = %hash1 => Column3. %hash3 = %hash2 => Column 4.

I would be thankful for any help/advice. Kind regards, Ila14 </>

In reply to Multidimensional hash help! by ila14

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