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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
Old 07-19-2011
Java 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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COLUMN(1)						    BSD General Commands Manual 						 COLUMN(1)

NAME
column -- columnate lists SYNOPSIS
column [-ntx] [-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. -n By default, the column command will merge multiple adjacent delimiters into a single delimiter when using the -t option; this option disables that behavior. This option is a Debian GNU/Linux extension. ENVIRONMENT
The COLUMNS, LANG, LC_ALL and LC_CTYPE environment variables affect the execution of column as described in environ(7). EXIT STATUS
The column utility exits 0 on success, and >0 if an error occurs. EXAMPLES
(printf "PERM LINKS OWNER GROUP SIZE MONTH DAY " ; printf "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. BUGS
Input lines are limited to LINE_MAX (2048) bytes in length. BSD
July 29, 2004 BSD
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