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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
Old 11-25-2016
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
 

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RTBL(3) 						   BSD Library Functions Manual 						   RTBL(3)

NAME
rtbl_create, rtbl_destroy, rtbl_set_flags, rtbl_get_flags, rtbl_set_prefix, rtbl_set_separator, rtbl_set_column_prefix, rtbl_set_column_affix_by_id, rtbl_add_column, rtbl_add_column_by_id, rtbl_add_column_entry, rtbl_add_column_entry_by_id, rtbl_new_row, rtbl_format -- format data in simple tables LIBRARY
The roken library (libroken, -lroken) SYNOPSIS
#include <rtbl.h> int rtbl_add_column(rtbl_t table, const char *column_name, unsigned int flags); int rtbl_add_column_by_id(rtbl_t table, unsigned int column_id, const char *column_header, unsigned int flags); int rtbl_add_column_entry(rtbl_t table, const char *column_name, const char *cell_entry); int rtbl_add_column_entry_by_id(rtbl_t table, unsigned int column_id, const char *cell_entry); rtbl_t rtbl_create(void); void rtbl_destroy(rtbl_t table); int rtbl_new_row(rtbl_t table); int rtbl_set_column_affix_by_id(rtbl_t table, unsigned int column_id, const, char, *prefix", const char *suffix); int rtbl_set_column_prefix(rtbl_t table, const char *column_name, const char *prefix); unsigned int rtbl_get_flags(rtbl_t table); void rtbl_set_flags(rtbl_t table, unsigned int flags); int rtbl_set_prefix(rtbl_t table, const char *prefix); int rtbl_set_separator(rtbl_t table, const char *separator); int rtbl_format(rtbl_t table, FILE, *file"); DESCRIPTION
This set of functions assemble a simple table consisting of rows and columns, allowing it to be printed with certain options. Typical use would be output from tools such as ls(1) or netstat(1), where you have a fixed number of columns, but don't know the column widths before hand. A table is created with rtbl_create() and destroyed with rtbl_destroy(). Global flags on the table are set with rtbl_set_flags and retrieved with rtbl_get_flags. At present the only defined flag is RTBL_HEADER_STYLE_NONE which suppresses printing the header. Before adding data to the table, one or more columns need to be created. This would normally be done with rtbl_add_column_by_id(), column_id is any number of your choice (it's used only to identify columns), column_header is the header to print at the top of the column, and flags are flags specific to this column. Currently the only defined flag is RTBL_ALIGN_RIGHT, aligning column entries to the right. Columns are printed in the order they are added. There's also a way to add columns by column name with rtbl_add_column(), but this is less flexible (you need unique header names), and is considered deprecated. To add data to a column you use rtbl_add_column_entry_by_id(), where the column_id is the same as when the column was added (adding data to a non-existent column is undefined), and cell_entry is whatever string you wish to include in that cell. It should not include newlines. For columns added with rtbl_add_column() you must use rtbl_add_column_entry() instead. rtbl_new_row() fills all columns with blank entries until they all have the same number of rows. Each column can have a separate prefix and suffix, set with rtbl_set_column_affix_by_id; rtbl_set_column_prefix allows setting the prefix only by column name. In addition to this, columns may be separated by a string set with rtbl_set_separator (by default columns are not seprated by anything). The finished table is printed to file with rtbl_format. EXAMPLES
This program: #include <stdio.h> #include <rtbl.h> int main(int argc, char **argv) { rtbl_t table; table = rtbl_create(); rtbl_set_separator(table, " "); rtbl_add_column_by_id(table, 0, "Column A", 0); rtbl_add_column_by_id(table, 1, "Column B", RTBL_ALIGN_RIGHT); rtbl_add_column_by_id(table, 2, "Column C", 0); rtbl_add_column_entry_by_id(table, 0, "A-1"); rtbl_add_column_entry_by_id(table, 0, "A-2"); rtbl_add_column_entry_by_id(table, 0, "A-3"); rtbl_add_column_entry_by_id(table, 1, "B-1"); rtbl_add_column_entry_by_id(table, 2, "C-1"); rtbl_add_column_entry_by_id(table, 2, "C-2"); rtbl_add_column_entry_by_id(table, 1, "B-2"); rtbl_add_column_entry_by_id(table, 1, "B-3"); rtbl_add_column_entry_by_id(table, 2, "C-3"); rtbl_add_column_entry_by_id(table, 0, "A-4"); rtbl_new_row(table); rtbl_add_column_entry_by_id(table, 1, "B-4"); rtbl_new_row(table); rtbl_add_column_entry_by_id(table, 2, "C-4"); rtbl_new_row(table); rtbl_format(table, stdout); rtbl_destroy(table); return 0; } will output the following: Column A Column B Column C A-1 B-1 C-1 A-2 B-2 C-2 A-3 B-3 C-3 A-4 B-4 C-4 HEIMDAL
June 26, 2004 HEIMDAL
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