Shell Programming and Scripting

Hi,

I have 2 files.

File 1

Code:

chr1  1234   2468   ABC
chr1  3456   4567   DEF
chr2  5643   6154   XYZ 
:
:
:
:
so on....

File 2

Code:

chr1  1500 2500   positive
chr1  2500 3500   negative
chr1  3000 4500   neutral
chr2  5800 6500   asterick

so on...

What I want is if the column 2 of file 2 is falling between columns 2 and 3 of file 1 then file 2 row should be assigned the value of column 4 of file1. Also it should consider the chr 1 in column 1, bcoz only those positions should be matched. (What i mean is if the column 2 of file 2 is falling between column 2 and 3 of different chromosome then it should not be assigned that gene. chr 1 of file 2 have to be matched to only chr1 of file 1)

output

Code:

chr1  1500 2500   positive         ABC
chr1  2500 3500   negative        DEF
chr1  3000 4500   neutral          DEF
chr2  5800 6500   asterick         XYZ

Thanks,

Diya

I think chr1 1500 2500 positive ABC shouldn't be in your output (1234 is not between 1500 and 2500). The same goes for chr2 5800 6500 asterick XYZ(5643 is not between 5800 and 6500)...

No, you are looking it the other way 1500-2500 of file 2 falls between 1234 and 2468. so it should be assigned ABC value in column 4. Same goes with the 4th row also.

Let me know if I am not clear.. I can explain more in detail

Thanks,

OK, then chr1 2500 3500 negative DEF shouldn't be in output, correct?

No, it should be in the output as part of it is between 3456 4567.

Does this make sense?

Thanks,

You wrote "if the column 2 of file 2 is falling between columns 2 and 3 of file 1". 2500 is the value of column 2 file 2 for this row. It does not fall between 3456 and 4567... Or am I missing something?

Sorry it should be if the range between column 2 and column3 of file 2 is falling between the range of column2 and column 3 of file 1 of the same chromosome then it should be assigned the name of column 4 in file 1 to file 2.

Thanks,

Diya