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Top Forums Shell Programming and Scripting Merging non-repeating columns of lines Post 302393641 by menenuh on Tuesday 9th of February 2010 09:31:37 AM
Old 02-09-2010
Merging non-repeating columns of lines

Hello,
I have file to work with. It has 5 columns. The first three, altogether, constitutes the position. The 4th column contains some values for downstream analysis and the fifth column contains some values that I want to add to 4th column (only if they happen to be in the same position).

My file looks like this:
Code:
chr3    10163261        10163262        A>R_32_32_50_22 rs71760202
chr3    10163295        10163296        A>R_28_28_50_20 rs71757232
chr3    10163295        10163296        A>R_28_28_50_20 rs71760202
chr3    10163306        10163307        T>Y_34_34_50_20 rs71757232
chr3    10163306        10163307        T>Y_34_34_50_20 rs71760202
chr3    10163306        10163307        T>Y_34_34_50_20 rs5030624

And I am trying to make it look like this:
Code:
chr3   10163261    10163262  A>R_32_32_50_22>rs71760202
chr3   10163295    10163296  A>R_28_28_50_20>rs71757232, rs71760202
chr3   10163306    10163307  T>Y_34_34_50_20>rs71757232, rs71760202, rs5030624

Any help / recommendation / pointer would be appreciated.
Cheers

Last edited by Scott; 02-09-2010 at 10:59 AM.. Reason: Code tags
 

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

NAME
column -- columnate lists SYNOPSIS
column [-entx] [-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 unless the -e option is used. 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. -e Do not ignore empty lines. 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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