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POScript to convert Huge Three column table into table
 

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  1. POScript to convert Huge Three column table into table
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    <p>I have a set of data (CSV files) in the following 3 column format:</p> <pre><code>A, B, C 3277,4733,54.1 3278,4741,51.0 3278,4750,28.4 3278,4768,36.0 3278,4776,50.1 3278,4784,51.4 3279,4792,82.6 3279,4806,78.2 3279,4814,36.4 </code></pre> <p>And I need to get a three-way contingency table like: (sorry, this doesn't look completely good)</p> <pre><code>A /B 4733 4741 4750 4768 4776 4784 4792 4806 4814 3277 C 54.1 3278 51 28.4 36 50.1 51.4 3279 82.6 78.2 36.4 </code></pre> <p>Similarly to an excel "pivot table", OpenOffice data pilot, or R "table(x,y,z)" </p> <p>The problem is that my dataset is HUGE (more than 500,000 total rows, with about 400 different factors in A and B. (OOo, MSO and R limits prevent from achieving this)</p> <p>I am sure a Python script could be used to create such a table. both A and B are numbers (but can be treated as strings). </p> <p>Anyone has dealt with this? (pseudocode or code in C or Java is also welcomed ... but I prefer python as it is faster to implement :)</p> <p><strong>Edit:</strong> Almost have it, thanks to John Machin. The following Python script <em>almost</em> provides what I am looking for, however, when writing the output file I can see that the values in the "headers" I am writing (taken from the first row) do not correspond to the other rows. </p> <pre><code>from collections import defaultdict as dd d = dd(lambda: dd(float)) input = open("input.txt") output = open("output.txt","w") while 1: line = input.readline() if not line: break line = line.strip('\n').strip('\r') splitLine = line.split(',') if (len(splitLine) &lt;3): break d[splitLine[0]][splitLine[1]] = splitLine[2] output.write("\t") for k,v in d.items()[0][1].items(): output.write(str(k)+"\t") output.write("\n") for k,v in d.items(): output.write(k+"\t") for k2,v2 in v.items(): output.write(str(v2)+"\t") output.write("\n") </code></pre>
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    1. COConsider using a numpy array, it's optimized for larger datasets http://www.scipy.org/Tentative_NumPy_Tutorial#head-d3f8e5fe9b903f3c3b2a5c0dfceb60d71602cf93
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    2. COI'm having trouble seeing the 3-way nature of this problem. Isn't your table just Z where Z[A,B] = C? And if you have 400 factors for A and B then Z is only 400*400. Are you averaging over identical A,B pairs? I'm missing a third dimension here. Much like roadkill.
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    3. COYes, sorry my description was wrong. I only need a mapping of the 3 column table to the row/column/value table. Ideally I need a script with takes a CSV file with A,B,C and write the same data in the shown tabular format.
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