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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 DEBIAN

ift-extract

I2M19058(1)							     GNU Info							       I2M19058(1)

NAME

       ift-extract.info - ift-extract.info

Built-in iSight firmware extractor and patcher
       ift-extract extract the Built-in iSight firmware from Apple driver and patch it to avoid some bugs in it. The firmware is then ready to get
       loaded into the chip using ift-load.

       * Menu:

       Finding the Apple driver: see "Driver"

       Command line options: see "Options"

       See also "Copying"

   1 Finding the Apple driver
       ift-extract extract Built-in iSight firmware from Apple iSight driver.  This driver is located at
       /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBVideoSupport.kext/Contents/MacOS/AppleUSBVideoSupport on your Mac OS X
       root partition.

       There is several version of this driver depending on driver version or host architecture (PowerPC or x86). Thus, ift-extract must determine
       know the variant of the driver in order to properly extract the firmware.

       Any AppleUSBVideoSupport file starting with those shipped with iMac G5 iSight must work. If not, please report unknown AppleUSBVideoSupport
       at bugreport mail address with machine type and OS X version.

   2 Command line options
       `-a' `--apple-driver' Apple driver filename where to extract the firmware.

       `-d' `--output-directory' The directory where to output the firmware. Defaults to /lib/firmware.

       `-f' `--output-filename' The output firmware name. Defaults to isight.fw

       `-?'  `--help' Shows option help and quit.

       Since ift-extract defaults to output the firmware to /lib/firmware/isight.fw, ensure you have the right to do so.

   3 Copying
       isight-firmware-tools is a project developped by A~Xtienne Bersac based on the work of Ronald S. Bultje, Johannes Berg and Ivan N. Zlatev.

       This manual has been written by A~Xtienne Bersac.

       Copyright (C) 2007 A~Xtienne Bersac <bersace@gmail.com>

perl v5.14.2							    2012-01-09							       I2M19058(1)
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