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Top Forums Shell Programming and Scripting Perl to extract values and print at end of each line Post 303035235 by k_manimuthu on Friday 17th of May 2019 02:59:55 AM
Old 05-17-2019
Your code regex part doesn't have reference for GT:PL value and need to modify the regex part.
Try the below code and you can add more regex based on your needs.

Code:
 perl -plane ' BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) } /^[^#].*AF1=(\d+\.?\d*);.*GT:PL\s*([^:]+):/ and $_ .= join "\t", ("",  sprintf("%1.2f",$1), $h{$2}, int($F[5]/33+0.5))' file

 

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UNSQUASHFS(1)						  uncompress squashfs filesystems					     UNSQUASHFS(1)

NAME
mksquashfs - tool to uncompress squashfs filesystems SYNOPSIS
unsquashfs [OPTIONS] FILESYSTEM [directories or files to extract] DESCRIPTION
Squashfs is a highly compressed read-only filesystem for Linux. It uses zlib compression to compress both files, inodes and directories. Inodes in the system are very small and all blocks are packed to minimize data overhead. Block sizes greater than 4K are supported up to a maximum of 64K. Squashfs is intended for general read-only filesystem use, for archival use (i.e. in cases where a .tar.gz file may be used), and in con- strained block device/memory systems (e.g. embedded systems) where low overhead is needed. OPTIONS
-v, -version print version, licence and copyright information. -d PATHNAME, -dest PATHNAME unsquash to PATHNAME, default "squashfs-root". -n, -no-progress don't display the progress bar. -no, -no-xattrs don't extract xattrs in file system. -x, -xattrs extract xattrs in file system (default). -p NUMBER, -processors NUMBER use NUMBER processors. By default will use number of processors available. -i, -info print files as they are unsquashed. -li, -linfo print files as they are unsquashed with file attributes (like ls -l output). -l, -ls list filesystem, but don't unsquash. -ll, -lls list filesystem with file attributes (like ls -l output), but don't unsquash. -f, -force if file already exists then overwrite. -s, -stat display filesystem superblock information. -e EXTRACT_FILE, -ef EXTRACT_FILE list of directories or files to extract. One per line. -da SIZE, -data-queue SIZE Set data queue to SIZE Mbytes. Default 256 Mbytes. -fr SIZE, -frag-queue SIZE Set fragment queue to SIZE Mbytes. Default 256 Mbytes. -r, -regex treat extract names as POSIX regular expressions rather than use the default shell wildcard expansion (globbing). Decompressors available gzip lzo xz SEE ALSO
mksquashfs(1) HOMEPAGE
More information about unsquashfs and the squashfs filesystem can be found at <http://squashfs.sourceforge.net/>. AUTHOR
squashfs was written by Phillip Lougher <plougher@users.sourceforge.net>. This manual page was written by Daniel Baumann <daniel.baumann@progress-technologies.net>. 4.2 2012-06-30 UNSQUASHFS(1)
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