Identify the overlapping and non overlapping regions

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# 1  
Old 02-17-2014
Identify the overlapping and non overlapping regions

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

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

if they (pos3 and pos4) wont overlap then output to output_2 file.
so if we compare file 1 with file2
2)chr1	1380	1480	6800	7800
3)chr1	6700	7700	1200	2200
4)chr2	8500	9500	5670	6670

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).
# 2  
Old 02-17-2014
Where are exactly are you stuck?
How far have you gotten so far?
# 3  
Old 02-17-2014
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
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