Replacing "." with "GG" in a certain column of a file that has heading Post: 302928486

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Top Forums UNIX for Dummies Questions & Answers Replacing "." with "GG" in a certain column of a file that has heading Post 302928486 by kush on Friday 12th of December 2014 05:52:27 AM

12-12-2014

Registered User

Replacing "." with "GG" in a certain column of a file that has heading

Hi, all, I have a file that looks like:

Code:

## XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX                              
## YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY                                            
#AA    AB    AC    AD    AE    AF    AG    AH    AI    AJ    AK    AL
20    60039    60039    T    C    1000    PASS    .    .    0|0    0|0    0|0
20    60097    60097    G    A    999    PASS    .    .    0|0    0|0    0|0

The file has two lines starting with ## - heading lines (## XXX and ## YYY). Third line from above starting with # - indicate names of the columns (AA, AB etc). And the rest of the lines - are values.

I need to replace "." to "GG" in the 9th column AI.
Heading should stay unchanged. File is lets say, tab-delimited.

Thank u for ur suggestion!
best, kush

Last edited by Scrutinizer; 12-13-2014 at 09:13 AM.. Reason: Modified incorrectly put code tags

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paste

PASTE(1)						      General Commands Manual							  PASTE(1)

NAME

       paste - paste multiple files together

SYNOPSIS

       paste [-s] [-d list] file...

OPTIONS

       -d     Set delimiter used to separate columns to list.

       -s     Print files sequentially, file k on line k.

EXAMPLES

       paste file1 file2   # Print file1 in col 1, file2 in col 2

       paste -s f1 f2	   # Print f1 on line 1 and f2 on line 2

       paste -d : file1 file2
			   # Print the lines separated by a colon

DESCRIPTION

       Paste  concatenates  corresponding  lines of the given input files and writes them to standard output. The lines of the different files are
       separated by the delimiters given with the option -s. If no list is given, a tab is substituted for every linefeed, except  the	last  one.
       If  end-of-file	is hit on an input file, subsequent lines are empty.  Suppose a set of k files each has one word per line.  Then the paste
       output will have k columns, with the contents of file j in column j.  If the -s flag is given, then the first file is on line 1, the second
       file on line 2, etc.  In effect, -s turns the output sideways.

       If  a list of delimiters is given, they are used in turn.  The C escape sequences 
, 	, \, and  are used for linefeed, tab, backslash,
       and the null string, respectively.

																	  PASTE(1)