Find columns in a file based on header and print to new file Post: 302986407

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Top Forums Shell Programming and Scripting Find columns in a file based on header and print to new file Post 302986407 by LMHmedchem on Friday 25th of November 2016 12:26:41 AM

11-25-2016

Registered User

Find columns in a file based on header and print to new file

Hello,

I have to fish out some specific columns from a file based on the header value. I have the list of columns I need in a different file. I thought I could read in the list of headers I need,

Code:

# file with header names of required columns in required order
headers_file=$2

# read contents of headers_file into array
IFS=$'\n' read -a headers_list < $headers_file

and then loop through the list to pick out each column I need,

Code:

# loop on header list
for header_value in "${headers_list[@]}"
do
   # print current input file
   echo $header_value

   # look for the column in the input file
   awk -v OFS='\t' -v column_header="$header_value" 'NR==1{for (i=1; i<=NF; i++) if ($i==column_header){p=i; break}; next} {print $p}' $input_file > $output_file

done

The above awk does not work and even if it did it would overwrite the data from each previous column found. How do I find all the columns I need and then print all of them in the right order so they all end up in the output file?

The only thing I could think of was to read the header line from $input_file into another array and then loop through $headers_list making a note of the numerical position of the columns I need. In theory, I could use the list of numerical positions to cobble together a cut argument to get the columns I need. That seems like it would be horribly messy syntax and could probably be done with one line of awk from someone who knows what they are doing.

That means it's time to post and ask for help. I found allot of topics like this one, but most of them seemed to find one column by the header value and print it.

In case that makes a difference, the input files I am working have < 200 columns but may have almost any number of rows. The input file is space delimited and the output should be tab delimited, though I could replace space with tab after the fact if necessary.

Suggestions would be greatly appreciated.

LMHmedchem

LMHmedchem

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lsns

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)