Shell Programming and Scripting

Try:

Code:

awk 'NR==FNR{a[$0]=$2;b[$0]=$3}NR!=FNR{for (i in a){if (($2>=a[i]&&$2<=b[i])||($3>=a[i]&&$3<=b[i])){print i" "$4}}}' file2 file1

Hi,

Firstly thanks for the solution. However it does not seem to be 100% proper for my requirement. In the above code I dont understand where are you checking for the same chr( chromosome) in 2 files?

for example

Code:

chr1    670944  671094  altPromoter     - LOC100133331
chr18   670323  674160  bleedingExon    - LOC100133331
chr18   670323  674160  bleedingExon    - DQ575786
chr18   670323  674160  bleedingExon    - DQ599872

In the above o/p LOC100133331 belongs to chr1 and chr18 based on the coordinates. but in real scenario if you take file 1 its only on chr1.

It should go by chr basis in both files. If the row on file 2 is on chr1 then only chr1 rows should be checked in file1 for assigning the column 4 value.

Is this been taken care of in the above code?

Thanks,

---------- Post updated 02-07-12 at 12:22 PM ---------- Previous update was 02-06-12 at 03:09 PM ----------

Hi,

Please let me know if I was not clear.. I can explain more in detail once again

Thanks,

Try this:

Code:

awk 'NR==FNR{a[$0]=$2;b[$0]=$3;}NR!=FNR{for (i in a){split(i,x," +");if (($1==x[1]&&$2>=a[i]&&$2<=b[i])||($3>=a[i]&&$3<=b[i])){print i" "$4}}}' file2 file1

Hi,

I tried the new code.. but still i dont find the difference between both outputs. What I feel is its not considering the chr name in column 1 of 2 files.. It needs to pick column 4 value only from the same chr in both files..

Thanks,