Shell Programming and Scripting

This is NOT what you specified in post#1:

Code:

Data_1 2 Z
Data_1 3 T
Data_1 10 A
Data_1 11 T

Yes as I mentioned, it will only work with single sequence line FASTA.
Try this instead, which should no work with a wrapped (multi-line) FASTA sequence:

Code:

awk '
  NR==FNR {
    R[$1,$2]=$3
    next
  }

  FNR>1 {
    h=$1
    len=length($2)
    print RS h
    for(i=2; i<=NF; i++) {
      s=x
      for(j=1; j<=len; j++) {
        pos=j+(i-2)*len
        s=s ((h,pos) in R ? R[h,pos] : substr($i,j,1))
      }
      print s
    }
  }
' FS='\t' file2 FS=" " RS=\> file1

Thanks for reminding, RudiC.
Sorry for my mistake.

I just edit my Post 1.
Thanks a lot.

So that means the sample of file2 also changes?

Also, your sample file2 is not TAB-delimited

I corrected post #16 so that it works for TAB delimited file2
Could you check the order and if the file is indeed TAB delimited

Thanks, Scrutinizer.

Might to know how to correct Syntax error issue again?
If I run it as a long awk command at terminal.
It will return Syntax error etc.

If I copy and paste the whole command to a file called "run.sh" and execute it as "sh run.sh".
It will still return some Syntax error

Sorry and thanks for your guide and advice.

---------- Post updated at 06:28 AM ---------- Previous update was at 06:25 AM ----------

Hi Scrutinizer,

File 1 is a one line long record Fasta file (Include a first line of header description and second line is its corresponding nucleotide sequence).
File 2 is a file got 3 column (Tab-delimited).
First column is the header description (without ">") of File 1;
Second column is the word to replace in File 1;
Third column is position of word to replace in File 1;

Basically it is still same as my original question.
Just I forget to mention that my file 2 is a tab-delimited file

Sorry for confusing.
I just edited my thread to clarify it.

---------- Post updated at 06:29 AM ---------- Previous update was at 06:28 AM ----------

My main objective is hope to replace all specific word in File 1 based on the record provided in File 2 (specific position and replace with new word based on File 2).

Yes but now your sample file2 does not match the description. Which one is right and if it is not the sample, could you correct the sample?

And you meant 3 fields presumably, not lines ...

Hi Scrutinizer,

I just edited my Post#1.
Is that make the thing clear now?

Basically I still have 2 Input File now.
The data I shown in Post#1 just a first few record as the whole file is around 2 million word.

Thanks.