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Top Forums Shell Programming and Scripting Identify the overlapping and non overlapping regions Post 302888830 by data_miner on Monday 17th of February 2014 03:06:27 PM
Old 02-17-2014
Identify the overlapping and non overlapping regions

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).
 

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diff3(1)						      General Commands Manual							  diff3(1)

NAME
diff3 - 3-way differential file comparison SYNOPSIS
file1 file2 file3 DESCRIPTION
compares three versions of a file, and prints disagreeing ranges of text flagged with these codes: all three files differ file1 is different file2 is different file3 is different The type of change required to convert a given range of a given file to some other is indicated in one of these ways: Text is to be appended after line number n1 in file f, where f = or Text is to be changed in the range line n1 through line n2. If n1 = n2, the range can be abbreviated to n1. The original contents of the range follows immediately after a indication. When the contents of two files are identical, the contents of the lower-numbered file is suppressed. Produces a script for the editor that can be used to incorporate into file1 all changes between file2 and file3 (see ed(1)); i.e., the changes that normally would be flagged and Produces a script to incorporate only changes flagged Produces a script to incorporate only changes flagged Produces a script that will incorporate all changes between file2 and file3, but treat overlapping changes (that is, changes that would be flagged with in normal listing) differently. The overlapping lines in both files will be inserted by the edit script bracketed by and lines. Produces a script that will incorporate only changes flagged , but treat these changes in the manner of option. The following command applies the resulting script to file1. EXTERNAL INFLUENCES
International Code Set Support Single- and multi-byte character code sets are supported. WARNINGS
Text lines that consist of a single period defeat Files longer than 64K bytes do not work. FILES
SEE ALSO
diff(1). diff3(1)
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