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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

dbs-edit-patch

DBS-EDIT-PATCH(1)						Debian Build System						 DBS-EDIT-PATCH(1)

NAME

       dbs-edit-patch - Edit a DBS patch

SYNOPSIS

       dbs-edit-patch [options] patch
       dbs-edit-patch -h|--help

DESCRIPTION

       dbs-edit-patch is script to generate or modify patches for Debian source-packages in DBS format.

WARNING

       dbs  is	deprecated,  please  switch  to  the  `3.0 (quilt)' Debian source package format instead. See http://wiki.debian.org/Projects/Deb-
       Src3.0#FAQ for a short guide how to do it.

OPTIONS

       -h, --help
	      Show summary of options.

       -t dir, --tmpdir=dir
	      Directory for the temporary files, default is /tmp or if set $TMP.

       -s dir, --sourcedir=dir
	      Top level directory of the debian-package source-tree, default is the present working directory.

       -P dir, --sourcepatchdir=dir
	      Directory containing upstream patches.

       -T dir, --sourcetardir=dir
	      Directory containing the upstream tarball.

       -p level, --strip=level
	      Striplevel -p of patch (Option -p of diff(1)), accepted values are 0 and 1, default is 0.

ENVIRONMENT VARIABLES

       TMP    Sets the directory for the temporary files, can be overridden with -t dir.

debian/vars
       dbs-edit-patch will automatically use variables defined in the optional debian/vars file.

       When a file debian/vars.in exists and debian/vars either does not exist or is older  than  any  of  the	following  files:  debian/vars.in,
       debian/changelog, debian/rules or debian/control, then dbs-edit-patch will try updating the vars file by running the following command
	   make -f debian/rules -W debian/vars.in debian/vars

EXAMPLES

       Edit the 021_debian patch of Heimdal:

	   ~/heimdal-0.3d> dbs-edit-patch -t/tmp 021_debian
	   Extracting source heimdal-0.3d.tar.gz ... successful.
	   Applying patch 001_replay ... successful.
	   etc.
	   Copying heimdal-0.3d to heimdal-0.3d-old ... successful.
	   Applying patch 021_debian ... successful.

       Edit  files under /tmp/021_debian/heimdal-0.3d as required, then put a short description into /tmp/021_debian/patch-description if desired,
       and finally execute /tmp/021_debian/dbs-update-patch to save the results.

       Technical  note:  dbs-edit-patch  extracts  all	patches  before  021_debian  into  /tmp/021_debian/heimdal-0.3d,  copies  the  result	to
       /tmp/021_debian/heimdal-0.3d-old,  and  applies the last patch 021_debian (if it exists). Also, it creates a shell script which will create
       the diff between the old and new directories:

	   ~/heimdal-0.3d> ls -la /tmp/021_debian
	   total 12
	   -rwxr-xr-x	 1 bam	    users	  112 Jan 31 13:31 dbs-update-patch*
	   -rw-r--r--	 1 bam	    users	    0 Jan 31 13:31 patch-description
	   drwxr-xr-x	14 bam	    users	 4096 Jan 31 13:31 heimdal-0.3d/
	   drwxr-xr-x	14 bam	    users	 4096 Jan 31 13:31 heimdal-0.3d-old/
	   drwxr-xr-x	 5 bam	    users	 4096 Jan 31 13:31 .stampdir/

	   ~/heimdal-0.3d> cat /tmp/021_debian/dbs-update-patch
	   #!/bin/sh -e
	   cd "/tmp/021_debian"
	   HOOK_DIR="/usr/src/heimdal/debian/dbs-hooks"
	   test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-prediff
	   find -name "*.bak" -print0 | xargs -0 --no-run-if-empty rm
	   find -name "*~" -print0 | xargs -0 --no-run-if-empty rm
	   : > new_patch
	   test ! -e patch-description || cp patch-description new_patch
	   diff -ruN heimdal-0.3d-old heimdal-0.3d >> new_patch || test $? -eq 1
	   mv new_patch  /usr/src/heimdal/debian/patches/021_debian
	   test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-postdiff

SEE ALSO

       diff(1), dbs(7), /usr/share/doc/dbs/

AUTHOR

       DBS was written by Adam Heath, modified by Ben Collins, modified and packaged for Debian by  Brian  May.  This  manpage	was  generated	by
       Andreas Metzler and modified by Robert Luberda.

Debian								February 15th, 2011						 DBS-EDIT-PATCH(1)
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