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Top Forums Shell Programming and Scripting Merging multiple files from multiple columns Post 302716471 by bartman2099 on Tuesday 16th of October 2012 12:19:53 PM
Old 10-16-2012
Merging multiple files from multiple columns

Hi guys,
I have very basic linux experience so I need some help with a problem.
I have 3 files from which I want to extract columns based on common fields between them.

File1:
Code:
--- rs74078040 NA 51288690 T G 461652 0.99223 0.53611 3
--- rs77209296 NA 51303525 T G 461843 0.98973 0.60837 3
--- rs7985170 NA 51304203 C T 461852 0.99215 0.541 3

File2:
Code:
id rsid chromosome pos allele_A allele_B index average_call info
--- rs74078040 NA 51288690 T G 461652 0.99852 0.52725 2
--- rs77209296 NA 51303525 T G 461843 0.99992 0.90562 2
--- rs7985170 NA 51304203 C T 461852 0.99994 0.93283 2
--- rs145780716 NA 19032912 G A 2054321 0.9988 0.026123 2

File3:
id rsid chromosome pos allele_A allele_B index average_call info
Code:
--- rs74078040 NA 51288690 T G 461652 0.956 0.8558 1
--- rs77209296 NA 51303525 T G 461843 0.9843 0.8989 1
--- rs7985170 NA 51304203 C T 461852 0.9323 0.6754 1
--- rs145780716 NA 19032912 G A 2054321 0.9098 0.7632 1

I want to take all the rows from File1 and say columns 1-7 (which are the same in all the files) and then add column 8 from File 2 and columns 9 and 10 from File3.
Note that File1 doesn't have a header but the other files do. Also, File1 has less lines than the other files which have the same number of lines.

The output would look like:
Code:
--- rs74078040 NA 51288690 T G 461652 0.99852 0.8558 1
--- rs77209296 NA 51303525 T G 461843 0.99992 0.8989 1
--- rs7985170 NA 51304203 C T 461852 0.99994 0.6754 1

Any help would be greatly appreciated.
Thanks!

Last edited by Franklin52; 10-17-2012 at 06:12 AM.. Reason: Please use code tags for data and code samples
 

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LSNS(8) 						       System Administration							   LSNS(8)

NAME
lsns - list namespaces SYNOPSIS
lsns [options] [namespace] DESCRIPTION
lsns lists information about all the currently accessible namespaces or about the given namespace. The namespace identifier is an inode number. The default output is subject to change. So whenever possible, you should avoid using default outputs in your scripts. Always explicitly define expected columns by using the --output option together with a columns list in environments where a stable output is required. Note that lsns reads information directly from the /proc filesystem and for non-root users it may return incomplete information. The cur- rent /proc filesystem may be unshared and affected by a PID namespace (see unshare --mount-proc for more details). lsns is not able to see persistent namespaces without processes where the namespace instance is held by a bind mount to /proc/pid/ns/type. OPTIONS
-J, --json Use JSON output format. -l, --list Use list output format. -n, --noheadings Do not print a header line. -o, --output list Specify which output columns to print. Use --help to get a list of all supported columns. The default list of columns may be extended if list is specified in the format +list (e.g. lsns -o +PATH). -p, --task pid Display only the namespaces held by the process with this pid. -r, --raw Use the raw output format. -t, --type type Display the specified type of namespaces only. The supported types are mnt, net, ipc, user, pid, uts and cgroup. This option may be given more than once. -u, --notruncate Do not truncate text in columns. -V, --version Display version information and exit. -h, --help Display help text and exit. AUTHORS
Karel Zak <kzak@redhat.com> SEE ALSO
nsenter(1), unshare(1), clone(2), namespaces(7) AVAILABILITY
The lsns command is part of the util-linux package and is available from https://www.kernel.org/pub/linux/utils/util-linux/. util-linux December 2015 LSNS(8)
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