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Top Forums Shell Programming and Scripting Obtain the names of the flanking regions Post 302810275 by anurupa777 on Tuesday 21st of May 2013 01:41:29 PM
Old 05-21-2013
Obtain the names of the flanking regions

Hi I have 2 files; usually the end position in the file1 is the start position in the file2 and the end position in file2 will be the start position in file1 (flanks)
Code:
file1
Id        start         end
aaa1    0           3000070
aaa1    3095270    3095341 
aaa1    3100822    3100894
aaa1    3167949    3168020
aaa1    3205652    3205723
aaa1    3684683    3684752

Code:
file2  
Id     start     end     name
aaa1  3000070  3095270  bbc
aaa1  3095341  3100822  rbc
aaa1  3100894  3137949  srh
aaa1  3137949  3167949  ytf

I want ot get some thing like this
Code:
output
Id     start      end    name1    name2
aaa1    3095270    3095341  bbc    rbc
aaa1    3100822    3100894  rbc    srh
----------------------------------

 

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COMBINE(1)																COMBINE(1)

NAME
combine - combine sets of lines from two files using boolean operations SYNOPSIS
combine file1 and file2 combine file1 not file2 combine file1 or file2 combine file1 xor file2 _ file1 and file2 _ _ file1 not file2 _ _ file1 or file2 _ _ file1 xor file2 _ DESCRIPTION
combine combines the lines in two files. Depending on the boolean operation specified, the contents will be combined in different ways: and Outputs lines that are in file1 if they are also present in file2. not Outputs lines that are in file1 but not in file2. or Outputs lines that are in file1 or file2. xor Outputs lines that are in either file1 or file2, but not in both files. "-" can be specified for either file to read stdin for that file. The input files need not be sorted, and the lines are output in the order they occur in file1 (followed by the order they occur in file2 for the two "or" operations). Bear in mind that this means that the operations are not commutative; "a and b" will not necessarily be the same as "b and a". To obtain commutative behavior sort and uniq the result. Note that this program can be installed as "_" to allow for the syntactic sugar shown in the latter half of the synopsis (similar to the test/[ command). It is not currently installed as "_" by default, but you can alias it to that if you like. SEE ALSO
join(1) AUTHOR
Copyright 2006 by Joey Hess <joey@kitenet.net> Licensed under the GNU GPL. moreutils 2012-04-09 COMBINE(1)
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