CODEWITHSUNDEEP
linuxubuntuawkreplacesed
everestial
everestial

Reputation: 7255

How to merge the given two line awk code into one line?

The data in my file are stored in columns. These columns contain specific values separated by ':'. I want to update the value if there is pipe '|' in either 6th or 8th column.

A line of my data is as follows:

0/1:38,59:97:99:.:.:2015,0,1366:0|1:.,.,.,.,.,.,.,.,.,.,.,.,.,.:1311:|:0.5  0/1:89,56:145:99:0|1:5238_G_C:2074,0,5187:.:.:.:.:. 0/1:31,65:96:99:.:.:2208,0,1170:.:.:.:.:.   0/1:58,74:132:99:.:.:2457,0,1761:.:.:.:.:.

In the input file there is a pipe in the first column at 8th field. So, the value of the 1st field gets updated by the value in the 8th field. There will be a pipe either at 6th or 8th field not at both. Pipe at other field positions doesn't matter. For the above input the expected output is: 

0|1:38,59:97:99:.:.:2015,0,1366:0|1:.,.,.,.,.,.,.,.,.,.,.,.,.,.:1311:|:0.5  0/1:89,56:145:99:0|1:5238_G_C:2074,0,5187:.:.:.:.:. 0/1:31,65:96:99:.:.:2208,0,1170:.:.:.:.:.   0/1:58,74:132:99:.:.:2457,0,1761:.:.:.:.:.

And, I have the following code:

First I update the value from 6th field

awk 'BEGIN{FS=OFS="\t"} {for (i=1;i<=NF;i++) { split($i,f,/:/); if (f[6]~/\|/) sub(/^[^:]+/,f[6],$i) } }1' 2ms01e_only.pHASER01.vcf > 2ms01e_PG_6th.pHASER01.vcf

and then update value from 8th position

awk 'BEGIN{FS=OFS="\t"} {for (i=1;i<=NF;i++) { split($i,f,/:/); if (f[8]~/\|/) sub(/^[^:]+/,f[8],$i) } }1' 2ms01e_PG_6th.pHASER01.vcf > 2ms01e_PG_transfered.pHASER01.vcf

How can I write above code (two separate lines) as one line? So, I can update the value in the first field if there is a pipe either in 6th or 8th field. btw, The updated value is pulled from 6th or 8th field. The given code does what I want to do but I have to do it two time. I just want a code that is one line.

Thanks,

Upvotes: 0

Views: 52

Answers (1)

James Brown
James Brown

Reputation: 37394

V2:

If you just want those 2 codes combined, this is one way:

awk 'BEGIN { FS=OFS="\t" } 
           { 
               for (i=1;i<=NF;i++) { 
                   split($i,f,/:/); 
                   if (f[6]~/\|/) 
                       sub(/^[^:]+/,f[6],$i);
                   if (f[8]~/\|/) 
                       sub(/^[^:]+/,f[8],$i);
               } 
           } 1' 2ms01e_only.pHASER01.vcf > 2ms01e_PG_6th.pHASER01.vcf

Untested.

Upvotes: 1

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