Snps annotation Post: 302990583

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Top Forums UNIX for Beginners Questions & Answers Snps annotation Post 302990583 by marwah on Saturday 28th of January 2017 09:35:05 PM

01-28-2017

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Snps annotation

I have the following Snps data

Code:

 CHROM	POS	ID
chr7	78599583	rs987435
chr15	33395779	rs987436
chr1	189807684	rs987437
chr20	33907909	rs987438
chr12	75664046	rs987439

and the following gene data

Code:

genename    name    chrom   strand  txstart txend
MAGI2	NM_001301128	chr7	-	77484309	78920826	77486567	78920572	21
MRPS18C	NM_001297769	chr4	+	84596108	84601900	84596254	84601206	5
MRPS18C	NM_001297767	chr4	+	84596108	84601900	84596254	84601374	5
GCOM1	NM_001018091	chr15	+	55671393	55797047	55671524	55794059	13
FAHD1	NM_001018104	chr16	+	1817225	1830204	1817231	1828128	3
FAM134B	NM_001034850	chr5	-	16526146	16670167	16527849	16670080	9

I'm trying to find the snp whose postion (POS) lie between the txstart and txend in the gene data
so for this data I have the first SNP will lie between MAGI2 txstart and txend

the out put should be

Code:

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

I have tried the following but it didn't work

Code:

awk '
FNR==1 {next}
FNR == NR {
        POS[++k]=$1
        ID[k]=$2
        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

snps data= pre_snoinfo_tumor.txt
gene dat=refFlat.txt

Last edited by marwah; 01-29-2017 at 05:10 AM..

marwah

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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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