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Full Discussion: Need help comparing Base Pairs within PERL
Top Forums Shell Programming and Scripting Need help comparing Base Pairs within PERL Post 302651297 by drossy on Tuesday 5th of June 2012 09:46:21 AM
Old 06-05-2012
Need help comparing Base Pairs within PERL
Hi I have a multi-step project I am working on and have been finding it difficult to come up with the correct approach.
The data I have been given resembles:

Code:
 
Index      Chr       Genotype   Mutation Type
1           Chr1           TT            Intronic
2           Chr1           AA            Exonic
3           Chr1           AG            Exonic
4           Chr1           CC            Frameshift
5           Chr1           CA            Intronic
...         ...              ....

My goal here is to compare a large file such as this one to a set of references that are a single letter (T,A,C,G). I need to split the genotype in the given file into two individual letters and then compare this to the reference. If either matches the reference, then the program should move on to the next reference. If, however, neither letter is consistant, then the program should give an output of the index number and mutation type that corresponds to that data.
I am still fairly new to this so all help would be greatly appreciated.
Thanks!
 

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LEARN ABOUT DEBIAN

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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