CODEWITHSUNDEEP
awk
gungu
gungu

Reputation: 161

How to transpose a repeating set of rows to columns using awk

Ive a text file with data in 7 columns in this format:

18030   AAJ51   FTO rs9939609   C__30090620_10  A   T
18030   AAJ51   CAT rs1001179   C__11468118_10  C   C
18030   AAJ51   CCL2    rs1024611   C___2590362_10  G   G
18030   AAJ51   TAS2R38 rs10246939  C___9506826_10  C   C
20287   AAJ51   FTO rs9939609   C__30090620_10  A   T
20287   AAJ51   CAT rs1001179   C__11468118_10  C   C
20287   AAJ51   CCL2    rs1024611   C___2590362_10  A   G
20287   AAJ51   TAS2R38 rs10246939  C___9506826_10  T   T

The 2nd, 3rd 4th and 5th columns are constant and repeat.

The variables are the 1st, 6th and 7th columns.

I would like to transpose the data in this way:

        FTO       CAT       CCL2        TAS2R38
        rs9939609 rs1001179 rs1024611   rs10246939
18030   AT        CC        GG          AT
20287   AT        CC        AG          TT

Whilst the example shows 4 rows per ID (the 5-digit number in first column is the ID) the actual file has 128 rows per ID so performing a match or regex would not be practical and prefer a method that iterates over a number of rows.

I saw this example on converting n number of rows but am unsure how to modify for this application.

UPDATE: CRLF endings can cause formatting problems which can be resolved using a tool like dos2unix

Upvotes: 2

Views: 374

Answers (2)

RomanPerekhrest
RomanPerekhrest

Reputation: 92904

GNU Awk solution:

awk '{ 
         if (!keys[$3]++) { b[++c] = $3; row1 = row1 OFS $3; row2 = row2 OFS $4 }
         line = groups[$1][$3];
         groups[$1][$3] = (line == ""? $6$7: line OFS $6$7) 
     }
     END{ 
         print row1 ORS row2; 
         for (i in groups) {
             r = i; 
             for (j in b) r = r OFS groups[i][b[j]];
             print r 
         } 
     }' OFS='\t' file | column -txn

The output:

       FTO        CAT        CCL2       TAS2R38
       rs9939609  rs1001179  rs1024611  rs10246939
18030  AT         CC         GG         CC
20287  AT         CC         AG         TT

Upvotes: 3

Zan Lynx
Zan Lynx

Reputation: 54393

Try using a last_seen variable and an array.

  1. When the last_seen variable changes, then output the array as a row.
  2. Store the values for the current row in the array.

Upvotes: 1

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