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Full Discussion: file comparison
Top Forums Shell Programming and Scripting file comparison Post 302700345 by paolo.kunder on Thursday 13th of September 2012 09:47:24 AM
Old 09-13-2012
file comparison
Dear All,
I would really appreciate if you can help me to resolve this file comparison

I have two files:


Code:
file1:
chr	start		end 		ID	gene_name
chr1	2020		3030		1	test1
chr1	900		5000		2	test1
chr2	5000		8000		3	test2
chr3	6000		12000		4	test3
chr3	6000		15000		5	test3

Code:
file2:
chr	start		end 		gene_name
chr1	2000		6000		test1
chr2	3500		9000		test2
chr3	5000		12000		test3

I would like to create a new file similar to file 1 but with the following criterias:
-the comparison should be made on column 4(gene_name)
-keep entries only if the difference between the second column of file 2 and file 1 is < of 1001; for example lane number 2 of file 1 is removed because the difference is 1100 (200-900)
-keep entries only if the third column of file 1 is equal or smaller of third column of file 2; for example fifth lane of lane 1 is removed because 15000 is greater than 12000

the output file should look like this:

Code:
file3:
chr	start		end 		ID	gene_name
chr1	2020		3030		1	test1
						
chr2	5000		8000		3	test2
chr3	6000		12000		4	test3

Any suggestion?
Thanks,
Paolo
 

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LEARN ABOUT DEBIAN

ecaccess-file-move

ECACCESS-FILE-MOVE(1p)					User Contributed Perl Documentation				    ECACCESS-FILE-MOVE(1p)

NAME

       ecaccess-file-move - Move or Rename ECaccess Files

SYNOPSIS

       ecaccess-file-move -version|-help|-manual

       ecaccess-file-move [-debug] source-ecaccess-file target-ecaccess-file

DESCRIPTION

       Allow moving an ECaccess File. When the move occurs within the same ECaccess File System then it is a rename. When the move occurs across
       two different ECaccess File Systems then first a copy is done and then a delete of the original file is done (e.g. similar to ecaccess-
       file-copy ... -erase).

       The source-ecaccess-file and target-ecaccess-file are in the form [domain:][/user-id/]path. Please read the "Shell commands -> File
       Management" section of the "ecaccess" guide for more information on the ECaccess File System.

ARGUMENTS

       source-ecaccess-file
	       The source ECaccess File name.

       target-ecaccess-file
	       The target ECaccess File name.

OPTIONS

       -version
	       Display version number and exits.

       -help   Print a brief help message and exits.

       -manual Prints the manual page and exits.

       -debug  Display the SOAP messages exchanged.

EXAMPLES

       ecaccess-file-move ec:test1.txt ec:test2.txt

       Rename the test1.txt file in the ECFS directory of the authenticated user in test2.txt.

       ecaccess-file-move ec:test1.txt home:test2.txt

       Copy the test1.txt file from the ECFS directory of the authenticated user to the test2.txt file in the $HOME directory of the authenticated
       user, then delete the test1.txt file from ECFS.

SEE ALSO

       ecaccess-file-delete, ecaccess-file-get, ecaccess-file-mget, ecaccess-file-modtime, ecaccess-file-mput, ecaccess-file-rmdir, ecaccess-file-
       copy, ecaccess-file-dir, ecaccess-file-mdelete, ecaccess-file-mkdir, ecaccess-file-chmod, ecaccess-file-put, ecaccess-file-size and
       ecaccess.

perl v5.14.2							    2012-04-16						    ECACCESS-FILE-MOVE(1p)
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