Using sed on 1st column of tab delimited file Post: 302540050

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Top Forums Shell Programming and Scripting Using sed on 1st column of tab delimited file Post 302540050 by Hkins552 on Tuesday 19th of July 2011 12:12:29 PM

07-19-2011

Registered User

Using sed on 1st column of tab delimited file

Hi all,
I'm new to Unix and work primarily in bioinformatics. I am in need of a script which will allow me to replace "1" with "chr1" in only the first column of a file which looks like such:

Code:

1       10327   rs112750067     T       C       .       PASS    ASP;RSPOS=10327;
SAO=0;SCS=0;SSR=0;VC=SNP;VP=050000000005000000000100;WGT=1;dbSNPBuildID=132
1       10433   rs56289060      A       AC      .       PASS    ASP;RSPOS=10433;
SAO=0;SCS=0;SSR=0;VC=INDEL;VP=050000000005000000000200;WGT=1;dbSNPBuildID=129

I would like it to be:

Code:

chr1       10327   rs112750067     T       C       .       PASS    ASP;RSPOS=10327;
SAO=0;SCS=0;SSR=0;VC=SNP;VP=050000000005000000000100;WGT=1;dbSNPBuildID=132
chr1       10433   rs56289060      A       AC      .       PASS    ASP;RSPOS=10433;
SAO=0;SCS=0;SSR=0;VC=INDEL;VP=050000000005000000000200;WGT=1;dbSNPBuildID=129

Any ideas?

Last edited by Scott; 07-19-2011 at 01:19 PM.. Reason: Please use code tags

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LEARN ABOUT SUSE

column

COLUMN(1)						    BSD General Commands Manual 						 COLUMN(1)

NAME

     column -- columnate lists

SYNOPSIS

     column [-tx] [-c columns] [-s sep] [file ...]

DESCRIPTION

     The column utility formats its input into multiple columns.  Rows are filled before columns.  Input is taken from file operands, or, by
     default, from the standard input.	Empty lines are ignored.

     The options are as follows:

     -c      Output is formatted for a display columns wide.

     -s      Specify a set of characters to be used to delimit columns for the -t option.

     -t      Determine the number of columns the input contains and create a table.  Columns are delimited with whitespace, by default, or with
	     the characters supplied using the -s option.  Useful for pretty-printing displays.

     -x      Fill columns before filling rows.

     Column exits 0 on success, >0 if an error occurred.

ENVIRONMENT

     COLUMNS  The environment variable COLUMNS is used to determine the size of the screen if no other information is available.

EXAMPLES

	   (printf "PERM LINKS OWNER GROUP SIZE MONTH DAY HH:MM/YEAR NAME
" 
	   ; ls -l | sed 1d) | column -t

SEE ALSO

     colrm(1), ls(1), paste(1), sort(1)

HISTORY

     The column command appeared in 4.3BSD-Reno.

AVAILABILITY

     The column command is part of the util-linux-ng package and is available from ftp://ftp.kernel.org/pub/linux/utils/util-linux-ng/.

BSD
								   June 6, 1993 							       BSD