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Full Discussion: How to use a loop for multiple files in a folder to run awk command?
Top Forums Shell Programming and Scripting How to use a loop for multiple files in a folder to run awk command? Post 302940849 by sajmar on Thursday 9th of April 2015 12:31:28 PM
Old 04-09-2015
How to use a loop for multiple files in a folder to run awk command?
Dear folks

I have two data set which there names are "final.map" and "1.geno" and look like this structures:
final.map:
Code:
gi|358485511|ref|NC_006088.3| 2044
 
 gi|358485511|ref|NC_006088.3| 2048
 gi|358485511|ref|NC_006088.3| 2187
 gi|358485511|ref|NC_006088.3| 17654
 
 gi|358485511|ref|NC_006088.3| 17666


1.geno:
Code:
gi|358485511|ref|NC_006088.3| 2048   G C 0 1 1
 gi|358485511|ref|NC_006088.3| 17654 A G 1 1 2
 
 gi|358485511|ref|NC_006088.3| 17666 A G 0 1 1
 
 gi|358485511|ref|NC_006088.3| 17785 G A 0 1 1
 gi|358485511|ref|NC_006088.3| 30347 G C 1 1 2


Now, I am trying to run this command below:

Code:
awk -f example.awk 1.geno final.map > 1.dat


In this command "example.awk" contains the below command:
NR==FNR{a[$1,$2]=$5" "$6" "$7;next}{print $1,$2,a[$1,$2]?a[$1,$2]:"0 0 0"}


the output of the awk command give us "1.dat" which is
Code:
gi|358485511|ref|NC_006088.3| 2044   0 0 0
 
gi|358485511|ref|NC_006088.3| 2048   0 1 1
 
 gi|358485511|ref|NC_006088.3| 2187   0 0 0
 
 gi|358485511|ref|NC_006088.3| 17654 1 1 2
 
 gi|358485511|ref|NC_006088.3| 17666 0 1 1




My problem is I have around 300 *.geno files which I want to get *.dat out of the awk command. I am knowing the loop in unix could be helpful but I think I am using the loop wrong in some way.

Could any one give me an idea how to avoid to run awk each time separately and do it at one time by looping?
Last edited by vgersh99; 04-09-2015 at 02:07 PM.. Reason: code tags, please!
 

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rmf

rmf(1mh)																  rmf(1mh)

Name
       rmf - remove folder

Syntax
       rmf [ +folder ] [ -help ] [ -[no]interactive ]

Description
       The  command  removes all of the messages within the current folder, and then removes the folder itself.  If there are any files within the
       folder which are not part of MH, they are not removed, and an error message is displayed.

       You can specify a folder other than the current folder by using the +folder argument.  If you do not specify a folder, and cannot find  the
       current folder, asks you whether you want to delete instead.

       If the current folder is removed, it makes current.

       Note that the command irreversibly deletes messages that do not have other links, so use it with caution.

       If  the folder being removed is a sub-folder, the parent folder becomes the new current folder, and tells you that this has happened.  This
       provides an easy mechanism for selecting a set of messages, operating on the list, then removing the list  and  returning  to  the  current
       folder from which the list was extracted.

       Using to delete a read-only folder deletes the private sequence and current message information from the file, without affecting the folder
       itself.	If you have sub-folders within a folder, you must delete all the sub-folders before you can delete the folder itself.

Options
       -help	 Prints a list of the valid options to this command.

       -interactive
       -nointeractive
		 Asks for confirmation before deleting a folder.  By default, deletes a folder and its messages without asking	for  confirmation.
		 If  you  specify  the	-interactive option, asks if you are sure before deleting the folder.  You are advised to use this option,
		 since when deletes a folder its contents are lost irretrievably.

Examples
       This example shows how asks for confirmation when the -interactive option is used:
       % rmf -interactive +test
       Remove folder "test"? y

Profile Components
       Path:   To determine the user's Mail directory

Files
       The user profile.

See Also
       rmm(1mh)

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