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Top Forums UNIX for Dummies Questions & Answers help! script to select line with greatest value 2 between columns Post 302566702 by wolf_blue on Thursday 20th of October 2011 11:59:10 PM
Old 10-21-2011
not working

I'm still getting a file with duplicate genes.

when I enter code:
Code:
nawk 'NR<2{next}{c=($NF-$(NF-1))}!($1 in A)||(c>m[$1]&&($1 in A)){m[$1]=c;A[$1]=$0 FS m[$1]}END{for(i in A) print A[i]}' yourfile

for a file like this:
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 end up getting genes that are written into the file as duplicates.
When I just want the longest gene with the greatest length to be written to one file.
I'm really grateful for your help.

Last edited by Franklin52; 10-21-2011 at 09:21 AM.. Reason: Please use code tags, thank you
 

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after(n)						       Tcl Built-In Commands							  after(n)

__________________________________________________________________________________________________________________________________________________

NAME
after - Execute a command after a time delay SYNOPSIS
after ms after ms ?script script script ...? after cancel id after cancel script script script ... after idle ?script script script ...? after info ?id? _________________________________________________________________ DESCRIPTION
This command is used to delay execution of the program or to execute a command in background sometime in the future. It has several forms, depending on the first argument to the command: after ms Ms must be an integer giving a time in milliseconds. The command sleeps for ms milliseconds and then returns. While the command is sleeping the application does not respond to events. after ms ?script script script ...? In this form the command returns immediately, but it arranges for a Tcl command to be executed ms milliseconds later as an event handler. The command will be executed exactly once, at the given time. The delayed command is formed by concatenating all the script arguments in the same fashion as the concat command. The command will be executed at global level (outside the context of any Tcl procedure). If an error occurs while executing the delayed command then the bgerror mechanism is used to report the error. The after command returns an identifier that can be used to cancel the delayed command using after cancel. after cancel id Cancels the execution of a delayed command that was previously scheduled. Id indicates which command should be canceled; it must have been the return value from a previous after command. If the command given by id has already been executed then the after can- cel command has no effect. after cancel script script ... This command also cancels the execution of a delayed command. The script arguments are concatenated together with space separators (just as in the concat command). If there is a pending command that matches the string, it is cancelled and will never be executed; if no such command is currently pending then the after cancel command has no effect. after idle script ?script script ...? Concatenates the script arguments together with space separators (just as in the concat command), and arranges for the resulting script to be evaluated later as an idle callback. The script will be run exactly once, the next time the event loop is entered and there are no events to process. The command returns an identifier that can be used to cancel the delayed command using after can- cel. If an error occurs while executing the script then the bgerror mechanism is used to report the error. after info ?id? This command returns information about existing event handlers. If no id argument is supplied, the command returns a list of the identifiers for all existing event handlers created by the after command for this interpreter. If id is supplied, it specifies an existing handler; id must have been the return value from some previous call to after and it must not have triggered yet or been cancelled. In this case the command returns a list with two elements. The first element of the list is the script associated with id, and the second element is either idle or timer to indicate what kind of event handler it is. The after ms and after idle forms of the command assume that the application is event driven: the delayed commands will not be executed unless the application enters the event loop. In applications that are not normally event-driven, such as tclsh, the event loop can be entered with the vwait and update commands. SEE ALSO
bgerror(n), concat(n), update(n), vwait(n) KEYWORDS
cancel, delay, idle callback, sleep, time Tcl 7.5 after(n)
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