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Full Discussion: Capturing column headers in an array
Top Forums Shell Programming and Scripting Capturing column headers in an array Post 302977864 by LMHmedchem on Friday 22nd of July 2016 03:09:36 PM
Old 07-22-2016
Capturing column headers in an array
Hello,

I am processing a tab delimited text file and need to grab all of the column headers in an array.

The input looks like,
Code:
num     Name            PCA_A1     PCA_A2       PCA_A3
0       compound_00     -3.5054     -1.1207     -2.4372
1       compound_01     -2.2641     0.4287      -1.6120
2       compound_02     -2.7516     -0.1016     -2.1137
3       compound_03     -1.3053     1.8495      -1.0224
4       compound_04     -1.1845     -0.3377     -2.9453
5       compound_05     -2.9492     -0.8277     -2.7023
6       compound_06     -0.6327     1.8127      -1.1693
7       compound_07     -0.2988     1.3539      -1.6114
8       compound_08     2.6872     -1.3726      -5.9732
9       compound_09     -1.4546     -0.8284     -3.5016

I captured the first line of the input with,
header_row=$(sed -n 1p "$input_file")

then I parsed "header_row" on tab,
IFS='\t' read -a column_headers <<< "$header_row"

If I print the size of the array, I get 1 and not 5.
Code:
# derive number of columns
number_of_columns=${#column_headers[@]}

echo "number_of_columns"
echo $number_of_columns

If I print the first array element, I get everything,

Code:
echo ${column_headers[0]}
num Name PCA_A1 PCA_A2 PCA_A3

I have tried parsing on space instead of tab in case the output of sed did not preserve the tabs,
IFS=' ' read -a column_headers <<< "$header_row"

but that gives me the same results. I am still ending up with the header row as a single string, not parsed into the elements of an array.

Any suggestions as to what I am doing wrong?

LMHmedchem
 

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mcxalter

mcxalter(1)							  USER COMMANDS 						       mcxalter(1)

  NAME
      mcxalter - various network transformations

  SYNOPSIS
      mcxalter [-imx <fname> (specify matrix input)] [-abc <fname> (specify label input)] [-tab <fname> (use tab file)] [-o <fname> (output)] [-tf
      spec (apply tf-spec to input matrix)]

  DESCRIPTION
      This utility supplies various transformations of networks.

  OPTIONS
      -abc <fname> (label input)
	The file name for input that is in label format.

      -imx <fname> (input matrix)
	The file name for input that is in mcl native matrix format.

      -tab <fname> (use tab file)
	This option causes the output to be printed with the labels found in the tab file.  With -abc this option will, additionally, construct  a
	graph  only on the labels found in the tab file.  If this option is used in conjunction with -imx the tab domain and the matrix domain are
	required to be identical.

      -tf <tf-spec> (transform input matrix values)
	Transform the input matrix values according to the syntax described in mcxio(5).

      -o fname (output file)
	Output file.

  AUTHOR
      Stijn van Dongen.

  SEE ALSO
      mcxio(5), mcx(1), mcxsubs(1), and mclfamily(7) for an overview of all the documentation and the utilities in the mcl family.

  mcxalter 12-068						      8 Mar 2012							 mcxalter(1)
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