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I tried in the following way {gsub("[\|]", "NA")}{gsub("[()]", "")} and it gives as INTRONMODIFIERNANANANACTDP1NAprotein_codingNACODINGNAENSCAFT00000000012NA11

But it should keep NA only where...

Sorry if i have put some stupid questions. I have tried doing that but couldn't find the logic as im novice in using awk.

Well!! I have tried that too, it still gives the same output.

---------- Post updated at 02:05 PM ---------- Previous update was at 01:59 PM ----------

Okay. Then could you help to do in the...

Thanks, i have the similar fix which is doing what i need. Here is the code.

awk 'BEGIN{OFS="\t"}{n=split ($8,TMP,";"); $8=""; for (i=1; i<=n; i++) if (match (TMP[i], /^DP=|^MQ=|^resource.EFF=/))...

In the initial question, 8th column is of type

chr1 602567 rs21953190 A G 5481.77 ....

This code is working only with first row. The second row remains the same. I want to replace the () and | in the 10th column in all the rows. i.e.
the data in the second row also should look like,

The previous solution



gives the output as



Here i want to split further

in first row into


similary the data in the second row

into


which means i want to replace...

Indeed the question looks similar, but the input format in the 8th column differs from the previous thread. To avoid confusion i have posted it as a new thread.

I have text file with lines as shown here. Each row has 11 columns separated by tab. In each row, i want to split the 8th column such that the output should look like shown below. Here value in the...

I tried to put the code as a oneliner as shown below,
awk '{n = split ($8,TMP,";") $8 = "" for (i=1; i<=n; i++) if (match (TMP[i], /^DP=|^MQ=|^SNPEFF/)) {sub (/^.*=/,"",TMP[i]); $8 = $8...

Thanks it works. Could you explain the code if possible?

Hi,

Thanks it is working. But it is not doing one thing. If you observe the output lines the 9th column is DP value and 10th is MQ value and then the values after SNPEFF_=.

Could you modify to...

chr1 412573 . A C 2758.77 . ...

Hi,

Thanks!! I found an alternate solution.


awk 'FNR==NR{a[$1]++;next}a[$1]' FileA FileB | awk -F '\t' 'BEGIN {OFS=FS} {print $0,"FIleA&FileB"}' > one.txt

awk...

Hi,

I have two files Files, FileA and FileB which are attached.Each row in the files have 8 tab delimited columns. The two files have to be compared and joined based on first two columns. The...

Thanks!! it worked.

Hi all,

I have a tab-delimited text file of size 10Mb. I am trying to count the number of lines using,

grep -c . sample.txtor
wc -l < sample.txt or
awk 'END {print NR}' sample.txtAll these...

Hi,

It worked and i too tried in the same way but, didn't put 1 in the end. What does it stand for?

Hi all,


I have a tab-delimited text file in which i have a few columns which look like,
X Y U V
2 3 4 5
4 5 3 4
6 4 3 2

For example, I want...

hii thanks !!!!!!!!!

It worked but need a little bit more help.

The awk code removes the alphabets [A-Z] in the 8th column and replaced with nothing. Could it be possible to keep those...

Please find the attached files.


awktest.txt is the original file and test1.txt is the file which was generated by using the commands posted by you in which only the identifiers are removed and...

Thanks for your answer.

I am sorry that i was not clear with the question.

The file is a tab-delimited text file with 8 columns and the 8th column having the text ...

Hi all,


I have a .vcf file which contains 8 coulmns and the data under each column as shown below,
CHROM POS ID REF ALT QUAL FILTER INFO ...