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Full Discussion: Awk-Group count of field
Top Forums Shell Programming and Scripting Awk-Group count of field Post 302278286 by patrick chia on Monday 19th of January 2009 11:36:18 PM
Old 01-20-2009
How to use the programming in UNIX to count the total G+C and the GC%?What command li
Seems like can use awk and perl command. But I don't have the idea to write the command line. Thanks for all of your advise.
For example, if I have the file whose content are:
Sample 1. ATAGCAGAGGGAGTGAAGAGGTGGTGGGAGGGAGCT
Sample 2. ACTTTTATTTGAATGTAATATTTGGGACAATTATTC
Sample 3. AAATCATGGTGGGTTTATTGATGGTTAGAAAGTTCC
All the sample above, got 36 nucleotide.

I want my output to count the G + C and GC %. So my output should look like this:
Sample 1: G+C = 21 GC%= 58.33%
Sample 2: G+C = 8 GC%=22.22%
Sample 3: G+C = 13 GC%=36.11%

Thanks and appreciate of your answer.
 

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LEARN ABOUT REDHAT

queue

queue(n)							Tcl Data Structures							  queue(n)

NAME

       queue - Create and manipulate queue objects

SYNOPSIS

       package require Tcl 8.2

       package require struct ?1.2.1?

       queueName option ?arg arg ...?

       queueName clear

       queueName destroy

       queueName get ?count?

       queueName peek ?count?

       queueName put item ?item ...?

       queueName size

DESCRIPTION

       The  ::struct::queue command creates a new queue object with an associated global Tcl command whose name is queueName.  This command may be
       used to invoke various operations on the queue.	It has the following general form:

       queueName option ?arg arg ...?
	      Option and the args determine the exact behavior of the command.	The following commands are possible for queue objects:

       queueName clear
	      Remove all items from the queue.

       queueName destroy
	      Destroy the queue, including its storage space and associated command.

       queueName get ?count?
	      Return the front count items of the queue and remove them from the queue.  If count is not specified, it defaults to 1.  If count is
	      1, the result is a simple string; otherwise, it is a list.  If specified, count must be greater than or equal to 1.  If there are no
	      items in the queue, this command will return count empty strings.

       queueName peek ?count?
	      Return the front count items of the queue, without removing them from the queue.	If count is not specified, it defaults to  1.	If
	      count  is  1,  the  result is a simple string; otherwise, it is a list.  If specified, count must be greater than or equal to 1.	If
	      there are no items in the queue, this command will return count empty strings.

       queueName put item ?item ...?
	      Put the item or items specified into the queue.  If more than one item is given, they will be added in the order they are listed.

       queueName size
	      Return the number of items in the queue.

KEYWORDS

       stack, matrix, tree, graph

struct								       1.2.1								  queue(n)
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