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Top Forums UNIX for Beginners Questions & Answers How to sum value of a column by range defined in another file awk? Post 303031523 by yifangt on Friday 1st of March 2019 02:01:43 PM
Old 03-01-2019
How to sum value of a column by range defined in another file awk?

I have two files, file1.table is the count table, and the other is the range condition file2.range.
Code:
file1.table
chr start end  count
N1 0 48  1
N1 48  181  2
N1 181 193  0
N1 193 326  2
N1 326 457  0
N1 457 471  1
N1 471 590  2
N1 590 604  1
N1 604 752  1
N1 752 875  1

Code:
file2.range
chr start end
N1      0     99
N1    100    199
N1    200    299
N1    300    399
N1    400    499
N1    500    599
N1    600    699
N1    700    799
N1    800    899
N1    900    999

The value in column 3 [correction: should be column 4] of file1 needs to be summed by the range defined in the file2 (sliding window), especially by column 2 (start position) of the range like this:
Code:
chr start end  count
N1      0     99    3
N1    100    199    2
N1    200    299    0
N1    300    399    0
N1    400    499    3
N1    500    599    1
N1    600    699    1
N1    700    799    0
N1    800    899    0
N1    900    999    0

There is a overlapping problem with some rows such as
Code:
N1 48  181  2 
N1 181 193  0

but I simply ignore it by choosing the start position [48] only at this moment.
Thanks a lot!

Last edited by yifangt; 03-04-2019 at 01:39 PM..
 

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DIFF3(1)						      General Commands Manual							  DIFF3(1)

NAME
diff3 - 3-way differential file comparison SYNOPSIS
diff3 [ -ex3 ] file1 file2 file3 DESCRIPTION
Diff3 compares three versions of a file, and publishes disagreeing ranges of text flagged with these codes: ==== all three files differ ====1 file1 is different ====2 file2 is different ====3 file3 is different The type of change suffered in converting a given range of a given file to some other is indicated in one of these ways: f : n1 a Text is to be appended after line number n1 in file f, where f = 1, 2, or 3. f : n1 , n2 c Text is to be changed in the range line n1 to line n2. If n1 = n2, the range may be abbreviated to n1. The original contents of the range follows immediately after a c indication. When the contents of two files are identical, the contents of the lower-numbered file is suppressed. Under the -e option, diff3 publishes a script for the editor ed that will incorporate into file1 all changes between file2 and file3, i.e. the changes that normally would be flagged ==== and ====3. Option -x (-3) produces a script to incorporate only changes flagged ==== (====3). The following command will apply the resulting script to `file1'. (cat script; echo '1,$p') | ed - file1 FILES
/tmp/d3????? /usr/lib/diff3 SEE ALSO
diff(1) BUGS
Text lines that consist of a single `.' will defeat -e. Files longer than 64K bytes won't work. DIFF3(1)
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