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Replacing characters in a file

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# 1  
Old 07-15-2014
Question Replacing characters in a file
Suppose I have a file which has 1000 columns (5 SHOWN FOR EXAMPLE)
two alphabets are separated by a space and then tab
Code:
A A"\t"C C"\t"G G"\t"0 0"\t"T T
A G"\t"C C"\t"G G"\t"A T"\t"0 0
G A"\t"0 0"\t"G C"\t"A A"\t"T C


whenever there is a 0 0 in any column, the output should be printed as

Code:
A A"\t"0 0"\t"G G"\t"0 0"\t"0 0
A G"\t"0 0"\t"G G"\t"0 0"\t"0 0
G A"\t"0 0"\t"G C"\t"0 0"\t"0 0


Can someone tell be how to solve this problem for 1000 columns.

Thank You in advance

Moderator's Comments:
Mod Comment Please select text first before pressing CODE tags button
Last edited by rossi; 07-15-2014 at 03:50 PM.. Reason: Removed excess CODE tags
# 2  
Old 07-15-2014
Hi, try:
Code:
awk '$0~s{$2=s; for(i=4; i<=NF; i++) $i=s}1' s="0 0" FS='\t' OFS='\t' file

Last edited by Scrutinizer; 07-15-2014 at 04:05 PM..
This User Gave Thanks to Scrutinizer For This Post:
rossi
# 3  
Old 07-15-2014
Not clear. What are the columns? Are those columns space separated or TAB separated? Your sample shows five, not four columns. Will Col three always be retained? What about Col 1000?

Please specify more carefully in English.
Last edited by RudiC; 07-15-2014 at 02:56 PM.. Reason: Nonsense!
# 4  
Old 07-15-2014
Hi

Sorry, the example has 5 columns.
Lets's take the 1st row
There is a space between A A, tab 0 0, tab G G, tab 0 0, tab T T.
Column three won't always be retained.

---------- Post updated at 06:58 PM ---------- Previous update was at 06:49 PM ----------

Hi,

Thank you so much, it tested it on the above example and it works.
Can you explain the code a bit. Like why is i=4, $2=s.

Thanks once again
# 5  
Old 07-15-2014
Hi, sure:
Code:
awk '
  $0~s {                         # if the line contains the search string in variable s
    $2=s                         # set the second field to that string 
    for(i=4; i<=NF; i++) $i=s    # and set field 4 and higher to that string (thus leaving only field 1 and 3 unchanged)
  }
  1                              # print the line
' s="0 0" FS='\t' OFS='\t' file  # set s (the search string variable) to "0 0" and 
                                 # and set both input and output field separators to TAB

This User Gave Thanks to Scrutinizer For This Post:
rossi
# 6  
Old 07-15-2014
Hi

I understand now from the comments what i=4 does in this example.

But what if I don't know the exact positions of the columns which has 0 0 in the 1000 column file. Let's suppose an example, column 4 doesn't have 0 0, column 5 has 0 0, no 0 0 in column 6 and 7, 0 0 in column 8 and so on.

What needs to be done in this case?
Hope that I was able to explain the situation a bit.

Thanks
# 7  
Old 07-15-2014
Let me guess: Is the requirement that if a column has "0 0" in any row, the entire column should become "0 0"? That would be an entirely different approach. You'd need to read the entire file to decide if any column goes zero and then print out all rows/columns.
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