Thank you all for the replies.

I can't seem to get the above working.

Here is some data, sorry this is hard to read but I thought it best to leave it in its original single space delimited format.

Code:

name col_1 col_2 col_3 col_4 col_5 col_6 col_7 col_8
name,1 2 1 1 0 1 0 11.75 9.6154
name,2 7 0 0 0 1 0 12.7917 8.6310
name,3 4 1 1 0.6 1 0 18.2769 4.6420
name,4 6 1 1 0 1 0 16.1389 7.7778
name,5 2 2 3 0.833333 1 0 21.5342 4.2924

headers_file,

Code:

col_1
col_6
col_3
col_4
col_8

desired output (in most cases, some columns in the original input will not be in output)

Code:

name	col_1	col_6	col_3	col_4	col_8
name,1	2	0	1	0	9.6154
name,2	7	0	0	0	8.6310
name,3	4	0	1	0.6	4.6420
name,4	6	0	1	0	7.7778
name,5	2	0	3	0.8333	4.2924

When I run the script above by I get,

Code:

col_1 col_1 col_1 col_1 col_1 col_1 
col_6 col_6 col_6 col_6 col_6 col_6 
col_3 col_3 col_3 col_3 col_3 col_3 
col_4 col_4 col_4 col_4 col_4 col_4 
col_8 col_8 col_8 col_8 col_8 col_8

The code suggestion posted by ripat has a similar issue but I haven't posted the results here because of the comment by Scrutinizer about the order of output.

I certainly should have included an example with my post, sorry about that. I am currently running this under cygwin 2.3.1 but this will also run on openSuse 13.2 x86_64.

I know that the term csv is sometimes used to refer to generic delimited text data and not just comma separated data. I stay away from comma separation because many of the fields I use (chemical names) have commas ( 1,1,4,4-tetrabutylpiperazine ). The values in the name column could also have unmatched single quotes ( N,N,N',N'-tetramethylguanidine ) or parenthesis ( 1-(2-aminoethyl)piperazine ). I think that code that replaces space with comma would be problematic in my particular case. Yet another reason why an example of real data would have been useful for me to post.

LMHmedchem