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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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RE_COMP(3)						     Linux Programmer's Manual							RE_COMP(3)

NAME
re_comp, re_exec - BSD regex functions SYNOPSIS
#define _REGEX_RE_COMP #include <sys/types.h> #include <regex.h> char *re_comp(const char *regex); int re_exec(const char *string); DESCRIPTION
re_comp() is used to compile the null-terminated regular expression pointed to by regex. The compiled pattern occupies a static area, the pattern buffer, which is overwritten by subsequent use of re_comp(). If regex is NULL, no operation is performed and the pattern buffer's contents are not altered. re_exec() is used to assess whether the null-terminated string pointed to by string matches the previously compiled regex. RETURN VALUE
re_comp() returns NULL on successful compilation of regex otherwise it returns a pointer to an appropriate error message. re_exec() returns 1 for a successful match, zero for failure. ATTRIBUTES
For an explanation of the terms used in this section, see attributes(7). +---------------------+---------------+-----------+ |Interface | Attribute | Value | +---------------------+---------------+-----------+ |re_comp(), re_exec() | Thread safety | MT-Unsafe | +---------------------+---------------+-----------+ CONFORMING TO
4.3BSD. NOTES
These functions are obsolete; the functions documented in regcomp(3) should be used instead. SEE ALSO
regcomp(3), regex(7), GNU regex manual COLOPHON
This page is part of release 4.15 of the Linux man-pages project. A description of the project, information about reporting bugs, and the latest version of this page, can be found at https://www.kernel.org/doc/man-pages/. GNU
2017-09-15 RE_COMP(3)
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