Dear Monks!

I am an early perl freshman. So far I do some text manipualtion in a line-by-line style on plain text documents. What I'd like to parse now is a table that needs to be rearranged so that info from a certain line goes to another place at another line. This line crossing is new to me and I can't get my head solving it...

Here is an example that I wrote to illustrate:

SNP5    IND1    A5    C5    0.8
SNP2    IND1    A2    C2    0.8
SNP1    IND1    A1    C1    0.8
SNP3    IND1    A3    C3    0.8
SNP4    IND1    A4    C4    0.8
SNP5    IND2    G5    T5    0.8
SNP2    IND2    G2    T2    0.8
SNP1    IND2    G1    T1    0.8
SNP3    IND2    G3    T3    0.8
SNP4    IND2    G4    T4    0.8

[download]

The last column (all the 0.8s) is not needed. And the first column (SNP1-5) is used to sort the info in columns 3 and 4 to the correct positions (columns 3 and 4 give possible states of SNP per IND). Each combination of IND and SNP is unique in this data. In my output I would like to get a table with a first column giving each IND, followed by the sorted info about its state for each SNP

This table needs to be stored as:

IND1    A1    C1    A2    C2    A3    C3    A4    C4    A5    C5
IND2    G1    T1    G2    T2    G3    T3    G4    T4    G5    T5

[download]

So I need to get from a multi-line format that stores the two possible states of IND per SNP, to a one-line format for every IND. Getting the SNPs sorted properly makes it possible to omit the name of the SNPs. They don't need to appear in the output. All I need is the right order (1-5 for each state).

My first strategy was to use hash tables to store each IND-SNP combination as key and each state combination as value. This works, but now I run into problems when I want to arrange the output table.

This is also the first time I do something with hash tables, so I am quite happy that I get my table populated already using this code:

while (<>) {

        @intarray = split('\t');

        $key = $intarray[1].",".$intarray[0];
        $value = $intarray[2].",".$intarray[3];

        $datahash{$key} = $value;
        }

[download]

I use commas as separators to possibly split the keys and values apart later on. The problem is just I don't know how to go on... I had to learn that I can't use regular expressions in calling values of a certain list of keys (like calling the values from any key matching ^IND1* in a foreach loop)... But also any other starting point to solve this reformatting challenge is highly appreaciated!

In reply to Table manipulation, array or hash? by robertkraus

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