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Old 11-19-2012, 11:49 AM   #1
Giorgio C
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Location: ITALY

Join Date: Oct 2010
Posts: 89
Default Editing a Kegg Ortholgy file for metagenomic analysis in Qiime

Hi all,

I'm trying to link a metagenomic analysis done with Qiime tools and a KO file obtained with Picrust. It's actually an editing text problem and
I guess someone here could help me.

I have this file (attached):

In the Column A there is a list od ID (often present in multiple time), every ID is associated with a number in column B.
The same numbers in column B correspond to the number of column D that is associeted with a functions (colum E,F,...).
So in other words the ID in column A should be associated with his function (in colum E,F..). The ID column and the functions columns are linked by the numbers in column B and D.

At the end I need to have something like this so:

K00001 Metabolism Enzyme Families Peptidases <tab> Organismal Systems Immune System Antigen processing and presentation <tab> .... (when mulitple entry)
..........
K0009 Metabolism Enzyme Families Peptidases


Acutally the column A should become in single entry ID only but without loosing the associated functions. As you can see some time there are single ID entry so it will have an only function associated like K0009 in the example.
Other time the ID entry are multiple like K0001 and so the function will be multiple and it need to be reported in the same raws tab separeted as shown up.

I know is a little bit tricky and complicated, I really hope to have been clear and that someone could help me.

Thanks a lot in advance,
Giorgio
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File Type: zip ko_to_pathway_qiime.txt.zip (79.4 KB, 3 views)
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