Building intervals Post: 302904417

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Top Forums UNIX for Dummies Questions & Answers Building intervals Post 302904417 by lsantome on Wednesday 4th of June 2014 04:45:01 AM

06-04-2014

Registered User

Building intervals

Hi all,

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!

Last edited by Franklin52; 06-04-2014 at 05:52 AM.. Reason: Please use code tags

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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)