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Full Discussion: Help needed editing text file using the terminal
Top Forums Shell Programming and Scripting Help needed editing text file using the terminal Post 302961748 by 4galaxy7 on Thursday 3rd of December 2015 07:04:50 AM
Old 12-03-2015
Help needed editing text file using the terminal
Hi,

I have text file with the header like this

tracking_id condition replicate FPKM
XLOC_000001 alpha 1 10.3199
XLOC_000001 alpha 0 10.3686
XLOC_000001 alpha 2 15.5619
...

With the first column being genes, the second being the condition, the third being the replicate number and the fourth being the relative gene expression. So I have about 15 000 genes tested, with three conditions (alpha, beta and low) and about between 11-13 replicates per condition (13 alpha, 11 beta and 11 low).

I want to change the format so along the top I have the 35 replicates along the top (i.e. the 13 alpha, 11 beta and 11 low), the genes down the side as they already are a FPKM value for each individual for each gene, something as follows

tracking_id 1 2 3 4 ..... 35
XLOC_00001 15 11 22 11 28
XLOC_00002 16 18 34 11 12
XLOC_00003 14 19 62 12 22
....
XLOC_15205

My knowledge of coding is v limited, so if someone could help me, either with a Perl script or a simple UNIX command line script, that would be really great.

Thanks!

Edit: I've added in a screen shot of the input (on the right) and what I want the output to look like. I did it in excel to make it a bit easier to see the columns, but I have them in text files too.

input

Code:
tracking_id condition replicate FPKM
XLOC_000001    alpha    1    10.3199
XLOC_000001    alpha    0    10.3686
XLOC_000001    alpha    2    15.5619
XLOC_000001    alpha    3    17.4901
XLOC_000001    alpha    4    5.73344
XLOC_000001    alpha    5    6.38582
XLOC_000001    alpha    6    13.2137
XLOC_000001    alpha    7    12.2629
XLOC_000001    alpha    8    9.99926
XLOC_000001    alpha    9    12.1221
XLOC_000001    alpha    10    10.5121
XLOC_000001    alpha    11    10.75
XLOC_000001    alpha    12    7.43817
XLOC_000001    alpha    13    7.36243
XLOC_000001    beta    0    12.5359
XLOC_000001    beta    1    11.2568
XLOC_000001    beta    2    10.0826
XLOC_000001    beta    3    9.53999
XLOC_000001    beta    4    7.37831
XLOC_000001    beta    5    5.46127
XLOC_000001    beta    6    7.86049
XLOC_000001    beta    7    7.86049
XLOC_000001    beta    8    11.8768
XLOC_000001    beta    9    13.6802
XLOC_000001    beta    10    9.68721
XLOC_000001    beta    11    9.03584
XLOC_000001    low    0    9.45804
XLOC_000001    low    1    9.54959
XLOC_000001    low    2    6.54958
XLOC_000001    low    3    3.23738
XLOC_000001    low    4    8.2976
XLOC_000001    low    5    5.60313
XLOC_000001    low    6    5.16253
XLOC_000001    low    7    6.5954
XLOC_000001    low    8    14.9347
XLOC_000001    low    9    9.66479
XLOC_000001    low    10    4.43241
XLOC_000001    low    11    5.78727
XLOC_000002    alpha    1    0
XLOC_000002    alpha    0    0
XLOC_000002    alpha    2    0
XLOC_000002    alpha    3    0
XLOC_000002    alpha    4    0
XLOC_000002    alpha    5    0
XLOC_000002    alpha    6    0
XLOC_000002    alpha    7    0.198545
XLOC_000002    alpha    8    0
XLOC_000002    alpha    9    0
XLOC_000002    alpha    10    1.50002
XLOC_000002    alpha    11    1.18404
XLOC_000002    alpha    12    0
XLOC_000002    alpha    13    0
XLOC_000002    beta    0    0
XLOC_000002    beta    1    0
XLOC_000002    beta    2    0.191399
XLOC_000002    beta    3    0.377084
XLOC_000002    beta    4    0
XLOC_000002    beta    5    0
XLOC_000002    beta    6    0
XLOC_000002    beta    7    0
XLOC_000002    beta    8    0
XLOC_000002    beta    9    0
XLOC_000002    beta    10    2.5607
XLOC_000002    beta    11    2.2376
XLOC_000002    low    0    0
XLOC_000002    low    1    0
XLOC_000002    low    2    1.37854
XLOC_000002    low    3    1.8105
XLOC_000002    low    4    2.57191
XLOC_000002    low    5    2.43143
XLOC_000002    low    6    0.777916
XLOC_000002    low    7    0.391041
XLOC_000002    low    8    0.545685
XLOC_000002    low    9    0.551643
XLOC_000002    low    10    0
XLOC_000002    low    11    0

output example. all the rows should look like the first two - i just had to add in a few spaces so they lined up correctly. and i just randomly added in the values into the table, but in the ouput they need to correspond to the FPKM values on the input.

Code:
tracking_id1(alpha) 2(alpha) 3(alpha) 4(alpha) 5(alpha) 6(alpha) 7(alpha) 8(alpha) 9(alpha) 10(alpha) 11(alpha) 1(beta) 2(beta
XLOC_000001     2    4    6    2    4    6    2    4    6    2    4    6 
XLOC_000002     2    4    6    2    4    6    2    4    6    2    4    6         
XLOC_000003    2    4    6    2    4    6    2    4    6    2    4    6    
XLOC_000004    2    5    4    2    5    4    2    5    4    2    5    4    
XLOC_000005    3    4    54    3    4    54    3    4    54    3    4    54    
XLOC_000006    2    1    5    2    1    5    2    1    5    2    1    5    
XLOC_000007    2    4    4    2    4    4    2    4    4    2    4    4    
XLOC_000008    2    4    6    2    4    6    2    4    6    2    4    6    
XLOC_000009    2    5    4    2    5    4    2    5    4    2    5    4    
XLOC_000010    3    4    54    3    4    54    3    4    54    3    4    54    
XLOC_000011    2    1    5    2    1    5    2    1    5    2    1    5    
XLOC_000012    2    4    4    2    4    4    2    4    4    2    4    4    
XLOC_000013    2    4    6    2    4    6    2    4    6    2    4    6    
XLOC_000014    2    5    4    2    5    4    2    5    4    2    5    4    
XLOC_000015    3    4    54    3    4    54    3    4    54    3    4    54    
XLOC_000016    2    1    5    2    1    5    2    1    5    2    1    5    
XLOC_000017    2    4    4    2    4    4    2    4    4    2    4    4    
XLOC_000018    2    4    6    2    4    6    2    4    6    2    4    6    
XLOC_000019    2    5    4    2    5    4    2    5    4    2    5    4    
XLOC_000020    3    4    54    3    4    54    3    4    54    3    4    54

Help needed editing text file using the terminal-screenshot-2015-12-03-12-10-27png
Help needed editing text file using the terminal-screenshot-2015-12-03-12-13-48png
Last edited by 4galaxy7; 12-03-2015 at 08:40 AM..
This User Gave Thanks to 4galaxy7 For This Post:
RavinderSingh13
 

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