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Full Discussion: search and count
Top Forums Shell Programming and Scripting search and count Post 302640349 by Diya123 on Monday 14th of May 2012 02:45:06 PM
Old 05-14-2012
Hi,

I have tried the above code with my original dataset and it does not seem to give me the right output. However the code runs perfect on the example file.. My original file is complex.. I have changed my files accordingly.

file1:
Code:
chr1    87333735        87334735
chr1    94522156        94523156
chr1    179102446       179103446
chr2    1230097 1231097
chr1    6342783 6343783
chr2    147131761       147132761
chr1    167787600       167788600
chr1    167853465       167854465
chr3    167867712       167868712
chr3    167870899       167871899

file2:
Code:
chr1	245025451	245025500
chr1	245025951	245026000
chr1	245026151	245026200
chr2	245027551	245027600
chr1	245027601	245027650
chr2	245027651	245027700
chr1	247003001	247003050
chr1	247047901	247047950
chr4	247048701	247048750
chr1	247050751	247050800
chr3	247051101	247051150
chr1	247061401	247061450
chr3	247071451	247071500

What I want is for each row in file 2 basing on column 1(chr1,chr2 etc) it has to check if it falls in the interval range of file1 column2 and column3 for the specific column1. In other words if file 2 column 1 is chr1 then it has to assign the rows to chr1 of file2 by assigning that many counts to file 1 column 4.

Let me know if I am not clear.

Thanks,
 

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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 5.10 3 Mar 2004 comm(1)
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