Shell Programming and Scripting

Hi Everyone,

Here's a snippet of my data:

File 1 = testRef2:

Code:

A1BG    -    13208    13284
AAA1    -    34758475    34873943
AAAS    -    53701240    53715412

File 2 = 42MLN.3.bedS2:

Code:

13208
13208
13360
13363
13484
13518
13518

My awk script:

Code:

awk 'NR == FNR{a[$1]=$1;next} {$1>=a[$3]}{$1<=a[$4]}{print $0}1' 42MLN.3.bedS2 testRef2

output:

Code:

A1BG    -    13208    13284
A1BG    -    13208    13284
AAA1    -    34758475    34873943
AAA1    -    34758475    34873943
AAAS    -    53701240    53715412
AAAS    -    53701240    53715412

What I was hoping to do is generate the following output:

Code:

A1BG    -    13208    13284
A1BG    -    13208    13284

Basically I want the data in $1 of File 2 to be >= [$3 of File 1] && <= [column $4 of File 1] and when it is then I want to print the lines from File 1.

Make sense?

Alternatively, I suppose simply appending the the string from $1 of File 1 to the end of the row in File 2 would also work.

Thanks for your help.