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Transpose a file

 
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# 1  
Old 06-29-2015
Transpose a file
Hello,
I have a file which looks like this

Input:
Code:
Sample    Genotype    Assay    Well    plate
Sample1    T    xx    A01    1
Sample2    T    xx    A01    2
Sample3    T    xx    A01    3
Sample4    T    xx    A02    4
Sample5    T    xx    A02    5
Sample6    T    xx    A02    6
Sample7    NA    xx    B01    7.2
Sample8    T    xx    B01    8
Sample9    T    xx    B01    9
Sample10    T    xx    B01    10
Sample11        xx    B01    11
Sample12    T    xx    B10    1
Sample13    T    xx    C01    2
Sample14    T    xx    C01    3
Sample15    T    xx    C01    4
Sample16    T    xx    C01    5
Sample17    T    xx    C01    6
Sample18    T    xx    C01    7.1
Sample19    C    xx    D02    8
Sample20    C    xx    D02    9
Sample21    T    xx    D02    11.1

and I need to transform it into a grid using three columns, "genotype", "well" as the top row and "plate" as the first column to get an output that looks like this
Code:
       1    2    3    4    5    6    7.1    7.2    8    9    10    11    11.1
A01    T    T    T                                        
A02                T     T    T                            
B01    NA    T    T    T                                    
B10    T                                                
C01        T    T    T    T    T    T                        
D02                                    C    C            T

I can do this with excel but there are 13 "plates" and over 500 "wells". Can this be done using unix? many thanks
# 2  
Old 06-29-2015
This is not really what I would call a simple transposing function (flipping columns to rows and vice-versa) but you are looking to tabulate the input.

You could use arrays if you can be certain of the rows & columns you want to look for. You can then read the input and set a flag in the appropriate row/column of the array depending on what you read. Finally, you display the table based on the array values, just looping round them.


What have you tried so far?
What are you comfortable using/supporting? For example ksh only, perl, awk, sed, C?

For "plate" do you mean the column marked "Assay"?

Can you logically define the process you want to follow? If you can then with refinement we can work out the code you need.


Sorry for the questions, but I would prefer to get a good solution that you can maintain in future rather than just going "Ta-da!" and you have no idea how it works and I have no idea if it meets your needs when you have data that is larger than the sample.




Robin
# 3  
Old 06-29-2015
No problem. So what I intend to do is layout a grid to know the "genotype" (2nd column) for each "well" (4th column) against the "plate" (5th column)

As I mentioned before, I have started doing it in excel

I have used awk/sed a couple of times before as one liner functions to delete columns, replace values

For "plate" I mean the last column which has thirteen variables ranging from 1 to 11.1

The file has approx 4000 rows. So the unique values for the last column, ie "plates" will always be 13 variables, in the range 1 to 11.1 and for the "wells" will always be 384 variables ranging from A01-A24, B01-B24, C01-C24.... to P01-P24.
# 4  
Old 06-29-2015
Adapted from a similar solution on this forum


Code:
awk     'NR>1{LN[$4]; HD[$5]; MX[$4,$5]=$2}
         END    {               printf "%8s", ""; for (i in HD) printf "%8s", i; print "";
                 for (j in LN) {printf "%8s",j;   for (i in HD) printf "%8s", MX[j,i]; print ""}
                }
        '  file

This User Gave Thanks to senhia83 For This Post:
nans
# 5  
Old 06-29-2015
Try
Code:
awk     'NR>1   {LN[$4]; HD[$5]; MX[$4,$5]=$2}
         END    {               printf "%10s", ""; for (i in HD) printf "%10s", i; print "";
                 for (j in LN) {printf "%10s",j;   for (i in HD) printf "%10s", MX[j,i]; print ""}
                }
        ' file
                            10       7.1       7.2      11.1         1         2         3         4         5         6         8         9
       C01                             T                                       T         T         T         T         T                    
       D02                                                 T                                                                     C         C
        11        xx                                                                                                                        
       A01                                                           T         T         T                                                  
       A02                                                                                         T         T         T                    
       B01                   T                  NA                                                                               T         T
       B10                                                           T

The line with "11" is there as your input file has a missing entry for it.
This User Gave Thanks to RudiC For This Post:
nans
 
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