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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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Trace(3pm)						User Contributed Perl Documentation						Trace(3pm)

NAME
Devel::Trace - Print out each line before it is executed (like "sh -x") SYNOPSIS
perl -d:Trace program DESCRIPTION
If you run your program with "perl -d:Trace program", this module will print a message to standard error just before each line is executed. For example, if your program looks like this: #!/usr/bin/perl print "Statement 1 at line 4 "; print "Statement 2 at line 5 "; print "Call to sub x returns ", &x(), " at line 6. "; exit 0; sub x { print "In sub x at line 12. "; return 13; } Then the "Trace" output will look like this: >> ./test:4: print "Statement 1 at line 4 "; >> ./test:5: print "Statement 2 at line 5 "; >> ./test:6: print "Call to sub x returns ", &x(), " at line 6. "; >> ./test:12: print "In sub x at line 12. "; >> ./test:13: return 13; >> ./test:8: exit 0; This is something like the shell's "-x" option. DETAILS
Inside your program, you can enable and disable tracing by doing $Devel::Trace::TRACE = 1; # Enable $Devel::Trace::TRACE = 0; # Disable or Devel::Trace::trace('on'); # Enable Devel::Trace::trace('off'); # Disable "Devel::Trace" exports the "trace" function if you ask it to: import Devel::Trace 'trace'; Then if you want you just say trace 'on'; # Enable trace 'off'; # Disable TODO
o You should be able to send the trace output to the filehandle of your choice. o You should be able to specify the format of the output. o You should be able to get the output into a string. We'll see. LICENSE
Devel::Trace 0.11 and its source code are hereby placed in the public domain. Author Mark-Jason Dominus (C<mjd-perl-trace@plover.com>), Plover Systems co. See the C<Devel::Trace.pm> Page at http://www.plover.com/~mjd/perl/Trace for news and upgrades. perl v5.14.2 2012-02-16 Trace(3pm)
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