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Full Discussion: reading information from a table and apply a command on multiple files
Top Forums Shell Programming and Scripting reading information from a table and apply a command on multiple files Post 302708825 by @man on Tuesday 2nd of October 2012 09:38:53 AM
Old 10-02-2012
MySQL reading information from a table and apply a command on multiple files
Hey gyuz,

I wanna calculate the number of mapped reads of a bam file in a region of interest. I used this code to do so :

Code:
samtools view input.bam chrname:region1 > region1.txt

This will store all the reads from given bam file within the region of interest in region1.txt

Now I have several bam files and several regions for each which are different. (regions are not the same in all bam files)

I prepared a list of them like below:

bam1 region1
bam1 region2
bam1 region3
bam2 region4
bam2 region4
bam3 region5

I want the script to read from the table and apply the function on proper bam file and regions and report the output for each region in a single file. region1.txt, region2.txt, region3.txt,.....

If you can help me with this you saved my time so much!!

Thanks in advance.
Last edited by @man; 10-02-2012 at 12:44 PM..
 

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LEARN ABOUT HPUX

show_link

show link(1m)															     show link(1m)

NAME

       show link - Displays attribute information about the specified soft link

SYNOPSIS

       cdscp show link link-name [attribute-name] [with attribute-name = attribute-value]

ARGUMENTS

       The  full  name	of  a  specific soft link.  The last simple name can contain wildcard characters.  The name of a particular attribute; see
       Description for valid attribute names.  The value of a particular attribute.

DESCRIPTION

       The show link command displays the names and values of the attributes specified in attribute-name.  You can use a combination of attributes
       in  any	sequence  in  a  single command. Use a space to separate multiple attributes.  You can use a with attribute-name = attribute-value
       clause to limit output only to soft links whose attributes have values equal to the specified values.  A space must precede and follow  the
       = (equals sign).  If you do not supply any attributes, the command displays all attributes and their values. The following is a description
       of soft link attributes: Specifies the creation timestamp (CTS) of this soft link Specifies the full name of the directory,  object  entry,
       or other soft link to which the soft link points Specifies a timeout value after which the soft link is either checked or deleted Specifies
       the timestamp of the most recent update to an attribute of the soft link

   Privilege Required
       You must have read permission to the soft link.	If you specify a wildcard soft link name, you also need read permission to  the  directory
       that stores the soft link.

NOTE

       This command is replaced at Revision 1.1 by the dcecp command and may not be provided in future releases of DCE.

EXAMPLE

       The  following command displays the current values of all the attributes associated with the soft link /.:/sales/region1.  cdscp> show link
       /.:/sales/region1

			       SHOW
			   SOFTLINK   /.../abc.com/sales/region1
				 AT   1991-10-15-15:54:40
			    CDS_CTS = 1991-10-15-19:54:35.00000003/08-00-2b-1c-8f-1f
			    CDS_UTS = 1991-10-15-19:54:35.00000006/08-00-2b-1c-8f-1f
		     CDS_LinkTarget = /.../abc.com/sales/service

			       SHOW
			   SOFTLINK   /.../abc.com/sales/region1
				 AT   1991-10-15-15:54:41
			    CDS_CTS = 1991-10-15-19:54:36.00000077/08-00-2b-1c-8f-1f
			    CDS_UTS = 1991-10-15-19:54:36.00000009/08-00-2b-1c-8f-1f
		     CDS_LinkTarget = /.../abc.com/sales/software
		    CDS_LinkTimeout = :
			 Expiration = 1991-10-15-00:00:00.0
			  Extension = +1-00:00:00.000

RELATED INFORMATION

       Commands: create link(1m), delete link(1m), list link(1m), remove link(1m), set link(1m)

																     show link(1m)
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