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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 REDHAT

ppmtosixel

ppmtosixel(1)						      General Commands Manual						     ppmtosixel(1)

NAME

       ppmtosixel - convert a portable pixmap into DEC sixel format

SYNOPSIS

       ppmtosixel [-raw] [-margin] [ppmfile]

DESCRIPTION

       Reads  a  portable  pixmap  as input.  Produces sixel commands (SIX) as output.	The output is formatted for color printing, e.g. for a DEC
       LJ250 color inkjet printer.

       If RGB values from the PPM file do not have maxval=100, the RGB values are rescaled.  A printer control header and a color assignment table
       begin the SIX file.  Image data is written in a compressed format by default.  A printer control footer ends the image file.

OPTIONS

       -raw   If  specified,  each  pixel  will  be explicitly described in the image file.  If -raw is not specified, output will default to com-
	      pressed format in which identical adjacent pixels are replaced by "repeat pixel" commands.  A raw file is often an order	of  magni-
	      tude larger than a compressed file and prints much slower.

       -margin
	      If  -margin  is not specified, the image will be start at the left margin (of the window, paper, or whatever).  If -margin is speci-
	      fied, a 1.5 inch left margin will offset the image.

PRINTING

       Generally, sixel files must reach the printer unfiltered.  Use the lpr -x option or cat filename > /dev/tty0?.

BUGS

       Upon rescaling, truncation of the least significant bits of RGB values may result in poor color conversion.  If the original PPM maxval was
       greater	than  100,  rescaling  also reduces the image depth.  While the actual RGB values from the ppm file are more or less retained, the
       color palette of the LJ250 may not match the colors on your screen.  This seems to be a printer limitation.

SEE ALSO

       ppm(5)

AUTHOR

       Copyright (C) 1991 by Rick Vinci.

								   26 April 1991						     ppmtosixel(1)
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