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Top Forums UNIX for Dummies Questions & Answers help! script to select line with greatest value 2 between columns Post 302566497 by wolf_blue on Thursday 20th of October 2011 12:43:30 PM
Old 10-20-2011
help! script to select line with greatest value 2 between columns

Hi,
I’m trying to do something I haven’t done before and I’m struggling with how to even create the command or script.
I have the following space delim file:

Code:
gene    accession    chr     chr_st    begin    end       
NN1        NC_024540    chr3    -    14000    14020    
NN1        NC_024543    chr3    -    14050    14060    
ATG        NC_01        chr12    +    12000    12100    
ATG        NC_02        chr12    +    12100    12300

This is an example file
I want to modify the file so that I only get the gene with the greatest length written to one file.
So want to calculate the length of each form of the genes in each row then: where length = end value- begin value

Code:
gene    accession    chr     chr_st    begin    end        length 
NN1        NC_024540    chr3    -    14000    14020    20
NN1        NC_024543    chr3    -    14050    14060    10
ATG        NC_01        chr12    +    12000    12100    100
ATG        NC_02        chr12    +    12100    12300    200

I want to be able to create a file with only the genes with greatest length which would look like this:
Code:
gene    accession    chr      chr_st    begin    end         length
NN1        NC_024540    chr3    -        14000    14020    20
ATG        NC_02        chr12    +        12100    12300    300

Any help is really aprreciated, I have 30,000 genes with different forms like this!
Thanks!

Last edited by zxmaus; 10-21-2011 at 04:41 AM.. Reason: added code tags
 

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SCRIPT-EMAIL(8) 					  System Administration Commands					   SCRIPT-EMAIL(8)

NAME
script-email - Amanda script to send email notifications DESCRIPTION
script-email is an Amanda script implementing the Script API. It should not be run by users directly. It sends a notification email to the addresses specified in the MAILTO property. PROPERTIES
This section lists the properties that control script-email's functionality. See amanda-scripts(7) for information on the Script API, script configuration. MAILTO List of email addresses that will receive an email on command execution. It is a multi-valued property: property "MAILTO" "amanda@domain.com" "sysadmin@domain.com" "amandauser@domain.com" EXAMPLE
In this example, script-email is scheduled to be run before the DLE, on the server. The unqualified email address amanda will be passed to the email system unchanged. The script is then attached to a dumptype, which can then be specified for any DLEs which require notification. define script-tool pre-email { comment "email me before this DLE is backed up" plugin "script-email" execute-on pre-dle-backup execute-where server property "mailto" "amanda" } define dumptype user-tar-email { user-tar script "pre-email" } SEE ALSO
amanda(8), amanda.conf(5), amanda-client.conf(5), amanda-scripts(7) The Amanda Wiki: : http://wiki.zmanda.com/ AUTHORS
Jean-Louis Martineau <martineau@zmanda.com> Zmanda, Inc. (http://www.zmanda.com) Dustin J. Mitchell <dustin@zmanda.com> Zmanda, Inc. (http://www.zmanda.com) Amanda 3.3.1 02/21/2012 SCRIPT-EMAIL(8)
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