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Top Forums Shell Programming and Scripting Perl to extract information from a file line by line Post 302981336 by cmccabe on Saturday 10th of September 2016 09:30:17 AM
Old 09-10-2016
In case this helps:
I just needed [,:] for an either "," or ";" match. Thank you Smilie.

Code:
 perl -plae '
     BEGIN{ %h = qw(0/0 hom 0/1 het 1/1 hom 1/2 het 2/2 hom) }
     /^[^#].*FDP=(\d+);.*STB=(\d+\.\d+)[,;].*([0-2]\/[0-2])/ and
     $_ .= join "\t", ("", ($2 >= 0.8 ? "STRAND BIAS" : "GOOD"), $1, $h{$3}, int($F[5]/33+0.5))' input


Last edited by cmccabe; 09-10-2016 at 10:30 AM.. Reason: fixed format
 

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LINTIAN-INFO(1) 					User Contributed Perl Documentation					   LINTIAN-INFO(1)

NAME
       lintian-info - give detailed information about Lintian's error tags

SYNOPSIS
       lintian-info [log-file...]

       lintian-info --tags tag ...

DESCRIPTION
       The lintian-info command parses the output of the lintian command and gives verbose information about the listed Lintian error tags, parses
       a Lintian override file and gives verbose information about the tags included, or (if given the -t or --tags option) explains a given tag
       or tags.

       If no log-file is specified on the command line, this command expects its input on stdin. Thus, the output of lintian can either be piped
       through lintian-info or a log file produced by lintian can be processed with this command.  (Note, though, that the lintian command has a
       command line option -i to display the same results as lintian-info, so you will not normally need to pipe the output of lintian into this
       command.)

OPTIONS
       -a, --annotate
	   Read from standard input or any files specified on the command line and search the input for lines formatted like Lintian override
	   entries.  For each one that was found, display verbose information about that tag.

       -h, --help
	   Display usage information and exit.

       --profile prof
	   Use the severities from the vendor profile prof when displaying tags.  If the profile name does not contain a slash, the default
	   profile for than vendor is chosen.

	   If not specified, lintian-info loads the best profile for the current vendor.

	   Please Refer to the Lintian User Manual for the full documentation of profiles.

       -t, --tags
	   Rather than treating them as log file names, treat any command-line options as tag names and display the descriptions of each tag.

EXIT STATUS
       If -t or --tags was given and one or more of the tags specified were unknown, this command returns the exit code 1.  Otherwise, it always
       returns with exit code 0.

SEE ALSO
       lintian(1)

AUTHORS
       Niels Thykier <niels@thykier.net>

       Richard Braakman <dark@xs4all.nl>

       Christian Schwarz <schwarz@monet.m.isar.de>

perl v5.14.2							    2013-02-16							   LINTIAN-INFO(1)
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