Shell Programming and Scripting

Code:

file1
chr	pos1	pos2	pos3	pos4
1)chr1	1000	2000	3000	4000 
2)chr1	1380	1480	6800	7800	
3)chr1	6700	7700	1200	2200	
4)chr2	8500	9500	5670	6670

Code:

file2
chr	pos1	pos2	pos3	pos4
1)chr2	8500	9500	5000	6000	
2)chr1	6700	7700	1200	2200
3)chr1	1380	1480	6700	7700
4)chr1	1000	2000	4900	5900

I have 2 input files file1 and file2 each containing 5 columns. The first column contains the chromosomes (range from 1-19,X of which only chr1 and chr2 were shown in example).
what i want to do is
condition1 if chr pos1 and pos2 in both files overlap
then i want to compare the pos3 and pos4. if they (pos3 and pos4) overlap i want to output them to output_1file
and

if they (pos3 and pos4) wont overlap then output to output_2 file.
so if we compare file 1 with file2

Code:

output_1file
2)chr1	1380	1480	6800	7800
3)chr1	6700	7700	1200	2200
4)chr2	8500	9500	5670	6670

Code:

output_2file
1)chr1	1000	2000	3000	4000

my definition of overlap
The positions need not be exactly same. They should contain common region atleast by 1bp(base pair).

Where are exactly are you stuck?
How far have you gotten so far?

The line numbers in 2 files are different (dont know which file is larger in terms of number of lines). so i was not able to compare them line by line which would have been a trivial task for me. i have to store the entire content of file 9chrand pos1-4) and then compare. i dint know how to do that that's why i asked in the forum given some instructions on how i can do that i will be able to come up with some thing