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Modify text file using awk

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# 15  
Old 05-23-2013
You had that fine command {gsub("[\\|()]", "\t")}. Why don't you split it to replace "\|" with "NA" and "[()]" with ""?
# 16  
Old 05-23-2013
Ubuntu
I tried in the following way
Code:
{gsub("[\|]", "NA")}{gsub("[()]", "")}

and it gives
Quote:
INTRON(MODIFIER||||CTDP1|protein_coding|CODING|ENSCAFT00000000012|11)
as
Code:
INTRONMODIFIERNANANANACTDP1NAprotein_codingNACODINGNAENSCAFT00000000012NA11

But it should keep NA only where there is no text i.e. in between |||||. But the above code replace NA wherever there is |. The output should look like
Code:
INTRON MODIFIER NA  NA  NA  CTDP1 protein_coding CODING ENSCAFT00000000012 11

---------- Post updated at 04:10 PM ---------- Previous update was at 03:21 PM ----------

Here is a fix, found in google.
Code:
awk 'BEGIN{OFS="\t"}{n=split ($8,TMP,";"); $8=""; for (i=1; i<=n; i++) if (match (TMP[i], /^DP=|^MQ=|^resource.EFF=/)) {sub (/^.*=/, "" ,TMP[i]); $12=$12 ($12?"\t":"") TMP[i]} {gsub("[\\|()]", "\t")}}1' file | awk 'BEGIN {FS=OFS="\t"} {for(i = 1; i <= NF; i++) {if(!$i) {$i = "NA" }}}1'
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