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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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comm(1) 							   User Commands							   comm(1)

NAME
comm - select or reject lines common to two files SYNOPSIS
comm [-123] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. If the input files were ordered according to the collating sequence of the current locale, the lines written will be in the collating sequence of the original lines. If not, the results are unspecified. OPTIONS
The following options are supported: -1 Suppresses the output column of lines unique to file1. -2 Suppresses the output column of lines unique to file2. -3 Suppresses the output column of lines duplicated in file1 and file2. OPERANDS
The following operands are supported: file1 A path name of the first file to be compared. If file1 is -, the standard input is used. file2 A path name of the second file to be compared. If file2 is -, the standard input is used. USAGE
See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes). EXAMPLES
Example 1 Printing a list of utilities specified by files If file1, file2, and file3 each contain a sorted list of utilities, the command example% comm -23 file1 file2 | comm -23 - file3 prints a list of utilities in file1 not specified by either of the other files. The entry: example% comm -12 file1 file2 | comm -12 - file3 prints a list of utilities specified by all three files. And the entry: example% comm -12 file2 file3 | comm -23 -file1 prints a list of utilities specified by both file2 and file3, but not specified in file1. ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE, LC_CTYPE, LC_MESSAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were successfully output as specified. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5) SunOS 5.11 3 Mar 2004 comm(1)
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