Snps annotation Post: 302990586

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Top Forums UNIX for Beginners Questions & Answers Snps annotation Post 302990586 by Don Cragun on Sunday 29th of January 2017 12:33:03 AM

01-29-2017

Registered User

Quote:

Originally Posted by marwah

you are so hard on me , by the way i'm not trying to confuse you or test your memory, I don't know how to modeify the code , If you can help please do so

I'm not trying to be hard on you. This site is here to help you and many, many others learn how to write code to do what you want or need to do. It is not here to act as your unpaid programming staff.

I didn't mean to imply that you were trying to confuse me or test me. I meant to say that copying someone's code without attribution and implying it is your own is plagiarism.

If you don't understand how that code works and what needs to be done to it to make it work with a different input file format, why don't you look at the awk man page on your system and try to figure out what the code is doing. If you can't figure it out, ask questions and the volunteers here will be happy to try to help you learn how it works and suggest what might need to be changed to work with your new file format.

Someone might also show you how to add a BEGIN clause to your awk script to print the heading you want in your output file. Maybe even something like:

Code:

awk '
BEGIN {	print "gene      ID        CHROM  POS       txstart      txend"
}
FNR == 1 {
	next
}
FNR == NR {
	POS[++k] = $2
	ID[k] = $3
	next
}
{	for(i = 1; i <= k; i++)
		if(POS[i] >= $5 && POS[i] <= $6)
			print $1, ID[i], $3, POS[i], $5, $6
}' pre_snpinfo_tumor.txt  refFlat.txt

As always, since you haven't bothered to tell us what operating system you're using, if you're using a Solaris/SunOS system change awk to /usr/xpg4/bin/awk or nawk.

With the sample input files you provided in post #1 in this thread, the above code produces the output:

Code:

gene      ID        CHROM  POS       txstart      txend
MAGI2 rs987435 chr7 78599583 77484309 78920826

exactly as requested.

Don Cragun

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LEARN ABOUT MINIX

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)