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append text to column in all files of directory

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# 1  
Old 06-14-2012
append text to column in all files of directory
Hi,

I want to append "chr" to all col 2 values of all files in a particular folder.
This is what I came up with but isnt working. Please help.

Code:
ls -1 * |
(
while read line
do
awk 'BEGIN {FS=OFS=":"} {$2="chr"$2;print $0}' $line > $line_new
done
)

Another question is, how to delete records from a file which have the same value in columns 3 through 39.

Thanks Much
# 2  
Old 06-14-2012
It is quite difficult to work from faulty code (syntax error on line 1).
Please post sample before and after data and explain the process in more detail.

Please post what Operating System and version you are running and what Shell this is.

Do you mean "append" or "prepend"?



For your "Another question", please open a new post and take note of the questions above before posting. What if you had to pay say £100,000 up-front to get the code written and had no contact with the programmers until after the program was written, what would you write in your Program Specification?
This User Gave Thanks to methyl For This Post:
alpesh
# 3  
Old 06-15-2012
bash
Hi,

Try this one,
Code:
cd path
for file in *
do
   awk 'BEGIN{FS=":";}{$2="chr"$2;a[NR]=$0;}END{for(i=1;i<=NR;i  ){print a[i] >FILENAME;}}' ${file}
done

this code snippet will update the changes in original file. If you want to create a new file then redirect to new file name..
Please post sample data else we wont do blindly... Anyway here my assumptions are,
1. field separator is :
2. chr string prefix or suffix, here i prefixed.
Cheers,
Ranga:-)
This User Gave Thanks to rangarasan For This Post:
alpesh
# 4  
Old 06-15-2012
Hi Methyl and Ranga,

I`m sorry for the inconvenience and many thanks for the help.

I`m using Red Hat Enterprise Linux 6 unix bash, thats all i know.

I have included the input and output this time. I need to do this with all files in the directory.

Input

Code:
Bak-2   1       711     T       C       38      6       1       1.28571
Bak-2   1       892     T       G       38      5       1       1
Bak-2   1       3279    G       T       30      3       1       1

Expected output

Code:
Bak-2   chr1       711     T       C       38      6       1       1.28571
Bak-2   chr1       892     T       G       38      5       1       1
Bak-2   chr1       3279    G       T       30      3       1       1

Ranga,

I ran your code, it is doing an infinite loop the printing line1 for file1 repeatedly.
Also I changed the delimiter to tabbed and used BEGIN{FS="\t";} in your code.

Output from Ranga`s code

Code:
Bak-2 chr1 711 T C 38 6 1 1.28571
Bak-2 chr1 711 T C 38 6 1 1.28571
Bak-2 chr1 711 T C 38 6 1 1.28571
Bak-2 chr1 711 T C 38 6 1 1.28571

Please help
# 5  
Old 06-15-2012
You need to set the output delimiter to TAB as well (FS=OFS="\t")
This User Gave Thanks to Scrutinizer For This Post:
alpesh
# 6  
Old 06-15-2012
Hi Scrutinizer,

I used this code


Code:
for file in *
do
   awk 'BEGIN{FS=OFS="\t"}{$2="chr"$2;a[NR]=$0;}END{for(i=1;i<=NR;i  ){print a[i] >FILENAME;}}' ${file}
done

It still gets into an infinite loop printing line1
# 7  
Old 06-15-2012
awk
Loop increment is missing there, so that the infinite loop occurs. I posted through mobile, something went wrong... Sorry for the inconvenience:-)
change the code as suggested by Scrutinizer... It will do the rest...
Happy weekend!
Cheers,
Ranga:-)
This User Gave Thanks to rangarasan For This Post:
alpesh
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