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Full Discussion: awk script to extract transcript information from gff3 file
Top Forums UNIX for Beginners Questions & Answers awk script to extract transcript information from gff3 file Post 303043938 by rdrtx1 on Tuesday 11th of February 2020 11:02:45 AM
Old 02-11-2020
Code:
awk '
(! h++) {print "transcript_id", "gene_name", "description", "chromosome", "strand", "transcript_start", "transcript_end", "gene_start", "gene_end";}
$9 ~ /ID=.*Name=/ {n=$9; sub(".*Name=", "", n); sub(";.*", "", n); gs[n]=$4; ge[n]=$5;}
$3~/.RNA/ {
n=$9; sub(".*Name=", "", n); sub(";.*", "", n);
p=$9; sub(".*Parent=", "", p); sub(";.*", "", p);
print n, p, "Desc", $1, $7, $4, $5, gs[p], ge[p];
}
' FS="\t" OFS="\t" input

Last edited by RavinderSingh13; 02-28-2020 at 01:51 AM..
This User Gave Thanks to rdrtx1 For This Post:
Maduranga
 

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LEARN ABOUT OPENSOLARIS

file-roller

file-roller(1)							   User Commands						    file-roller(1)

NAME

       file-roller - create, view, modify, or unpack an archive

SYNOPSIS

       file-roller  [--add]  [--add-to=archive]  [--default-dir=folder]  [--extract]  [--extract-here] [--extract-to=folder] [--force] [gnome-std-
       options]

DESCRIPTION

       The File Roller application enables you to create, view, modify, or unpack an archive. An archive is a file that acts as  a  container  for
       other files. An archive can contain many files, folders, and subfolders, usually in compressed form.

OPTIONS

       The following options are supported:

       -d, --add		       Ask for the name of the archive, then add the files, then quit the application.

       -a, --add-to=archive	       Add files to the specified archive, then quit the application.

       --default-dir=folder	       Specify the default folder for the --add and --extract options.

       -f, --extract		       Ask for the name of the destination folder, then extract the files, then quit the application.

       -h, --extract-here	       Extract archives using the archive name as destination folder and quit the program.

       -e, --extract-to=folder	       Extract archives to the specified folder, then quit the application.

       --force			       Create the destination folder without asking for confirmation.

       gnome-std-options	       Standard  options available for use with most GNOME applications.  See gnome-std-options(5) for more infor-
				       mation.

EXAMPLES

       Example 1: Unpacking an Archive

       example% file-roller --extract archive

EXIT STATUS

       The following exit values are returned:

       0	Application exited successfully

       >0	Application exited with failure

FILES

       The following files are used by this application:

       /usr/bin/file-roller    Executable for File Roller application.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNW			   |
       +-----------------------------+-----------------------------+
       |Interface stability	     |Volatile			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       File Roller Manual

       ar(1), tar(1), unzip(1), zip(1), attributes(5), gnome-std-options(5)

NOTES

       Written by Laszlo Kovacs, Sun Microsystems Inc., 2003, 2004, 2007.

SunOS 5.11							    08 Nov 2007 						    file-roller(1)
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