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foreach variable used in awk (please help!!)

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# 1  
Old 01-11-2010
foreach variable used in awk (please help!!)
I have a list of markers, say marker.txt:
Code:
rs913257
rs1018390
rs764180

and I need to know which ROW that each marker appears in another map file, say map.txt:
Code:
a rs12354060
b rs913257
c rs6650104
d rs2185539
e rs6681105
f rs1018390
g rs764180
h rs12564807
i rs3094315

The result shall return:
Code:
2
6
7

My marker_row.csh is like this:
Code:
#! /bin/csh -f

foreach marker (`more marker.txt`)
    awk -F, '{FS=" "; if($2==$marker) print NR}' map.txt
end

but returns me nothing!

Please help! Appreciate a lot!!
Last edited by Scott; 01-11-2010 at 08:19 PM.. Reason: Added code tags
# 2  
Old 01-11-2010
Hi.

This is in awk (nothing CSH about it):

Code:
$ awk 'NR == FNR { A[$2] = NR; next } A[$1] { print A[$1]}' map.txt markers
2
6
7

For both, you could use:
Code:
grep -f markers -n file1
2:rs913257
6:rs1018390
7:rs764180

Last edited by Scott; 01-11-2010 at 08:21 PM.. Reason: Updated because the question changed
# 3  
Old 01-11-2010
Quote:
Originally Posted by scottn
Hi.

This is in awk (nothing CSH about it):

Code:
$ awk 'NR == FNR { A[$1] = NR; next } A[$1] { print A[$1]}' map.txt markers
2
6
7

For both, you could use:
Code:
grep -f markers -n file1
2:rs913257
6:rs1018390
7:rs764180

Great. Thanks a lot! Scott. So seems there's no way allowing me to use a 'foreach' variable in 'awk', as the way I did it, right?
# 4  
Old 01-11-2010
Code:
awk 'NR==FNR {a[$1]++; next} ($2 in a) {print FNR} ' marker.txt map.txt

# 5  
Old 01-11-2010
The foreach construct you mentioned is a shell construct. In awk, you'd use something like

Code:
for( ELEMENT in ARRAY )

Doing this wholly inside awk is quicker than doing it in the shell.

And I'd recommend not using the C-Shell - period - which is why I did it in awk Smilie
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