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Top Forums Shell Programming and Scripting Find columns in a file based on header and print to new file Post 302986437 by drl on Friday 25th of November 2016 08:33:26 AM
Old 11-25-2016
Hi.

From my perspective, this is a csv manipulation problem. Consequently, a simple csv-aware tool seems appropriate. The dataset is transformed to csv format, and the header-name lines are collected into a csv-like string. The named columns are extracted, and the file is converted from csv format to TAB-separated format -- which the OP required,

Collecting these all together in a script and using dataset from ripat:
Code:
#!/usr/bin/env bash

# @(#) s1       Demonstrate extraction of fields, csvtool.

# Utility functions: print-as-echo, print-line-with-visual-space, debug.
# export PATH="/usr/local/bin:/usr/bin:/bin"
LC_ALL=C ; LANG=C ; export LC_ALL LANG
pe() { for _i;do printf "%s" "$_i";done; printf "\n"; }
pl() { pe;pe "-----" ;pe "$*"; }
em() { pe "$*" >&2 ; }
db() { ( printf " db, ";for _i;do printf "%s" "$_i";done;printf "\n" ) >&2 ; }
db() { : ; }
C=$HOME/bin/context && [ -f $C ] && $C dixf sed pass-fail
pe
dixf csvtool

FILE=${1-data1}
E=expected-output.txt
H=headers

pl " Input data file $FILE:"
head $FILE

pl " Input file converted to csv:"
sed -r 's/\s+/,/g' $FILE |
tee t1

pl " Header name file $H, name list:"
head $H
h1=$( paste -s -d, $H )
pe " Header list = $h1"

pl " Expected output:"
cat $E

pl " Results, extract columns, convert csv to TAB-spaced:"
csvtool namedcol $h1 t1 |
tee t2 |
sed -r 's/,/\t/g' |
tee f1

pl " Verify results if possible:"
C=$HOME/bin/pass-fail
[ -f $C ] && $C || ( pe; pe " Results cannot be verified." ) >&2

exit 0

producing:
Code:
$ ./s1

Environment: LC_ALL = C, LANG = C
(Versions displayed with local utility "version")
OS, ker|rel, machine: Linux, 3.16.0-4-amd64, x86_64
Distribution        : Debian 8.6 (jessie) 
bash GNU bash 4.3.30
dixf (local) 1.21
sed (GNU sed) 4.2.2
pass-fail (local) 1.9

csvtool tool for performing manipulations on CSV files from sh... (man)
Path    : /usr/bin/csvtool
Version : - ( /usr/bin/csvtool, 2014-08-06 )
Type    : ELF 64-bit LSB executable, x86-64, version 1 (SYSV ...)
Help    : probably available with --help
Home    : https://github.com/Chris00/ocaml-csv

-----
 Input data file data1:
H1 H2 H3 H4
01 02 03 04
11 12 13 14
21 22 23 24
31 32 33 34

-----
 Input file converted to csv:
H1,H2,H3,H4
01,02,03,04
11,12,13,14
21,22,23,24
31,32,33,34

-----
 Header name file headers, name list:
H3
H4
H1
H2
 Header list = H3,H4,H1,H2

-----
 Expected output:
H3      H4      H1      H2
03      04      01      02
13      14      11      12
23      24      21      22
33      34      31      32

-----
 Results, extract columns, convert csv to TAB-spaced:
H3      H4      H1      H2
03      04      01      02
13      14      11      12
23      24      21      22
33      34      31      32

-----
 Verify results if possible:

-----
 Comparison of 5 created lines with 5 lines of desired results:
 Succeeded -- files (computed) f1 and (standard) expected-output.txt have same content.

The command csvtool can be found in the Debian repository or at github as noted.

@LMHmedchem: with 300 posts, you should know that posting data samples, expected output, and your computing environment will help make replies easier and more likely to be applicable to your situation. Please do that in your future posts.

Best wishes ... cheers, drl
These 3 Users Gave Thanks to drl For This Post:
 

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