I hope you can help me with the following question:
I have multiple tables like this:
Code:
Chr Start End Zygosity Gene
chr1 153233510 153233510 het LOR
chr1 153233615 153233615 hom LOR
chr1 153233701 153233701 hom LOR
chr1 153233728 153233728 hom LOR
chr1 153233734 153233734 hom LOR
chr1 153234295 153234295 het LOR
chr1 153234602 153234602 hom LOR
chr1 155205331 155205331 hom GBA
chr1 155205669 155205669 hom GBA
chr1 155208647 155208647 het GBA
chr1 155208647 155208647 hom GBA
chr1 155209338 155209341 het GBA
chr1 155209341 155209341 hom GBA
chr1 155209360 155209360 het GBA
chr1 155214473 155214473 hom GBA
chr2 159831015 159831015 hom TANC1
chr2 128018063 128018063 het ERCC3
chr2 128018192 128018192 hom ERCC3
chr2 128018916 128018917 hom ERCC3
chr2 128018919 128018919 hom ERCC3
chr2 128018920 128018920 hom ERCC3
chr2 128018926 128018927 het ERCC3
chr2 128018928 128018928 het ERCC3
chr2 128018930 128018930 het ERCC3
chr2 128019178 128019178 hom ERCC3
chr2 128047101 128047101 hom ERCC3
chr2 128048142 128048142 hom ERCC3
chr2 128050134 128050134 hom ERCC3
What I need to do is to find, for every group in the "Gene" column, correlative lines where "Zygosity"=hom (there must be more than one per group). Once it's done, the interval is defined by the "Chr" value, "Start" value of the first element and the "End" value of the last element.
The expected output for the example above should be:
Code:
Chr Start End Gene Width
chr1 153233615 153233734 LOR 119
chr1 153234602 155205669 GBA 1971067
chr2 128018192 128018920 ERCC3 728
chr2 128019178 128050134 ERCC3 30956
I'm not asking for a complete solution but a hint to start. All suggestions are welcome.
Thamks!
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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)