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Full Discussion: Perl to update field based on a specific set of rules
Top Forums Shell Programming and Scripting Perl to update field based on a specific set of rules Post 303000872 by cmccabe on Friday 21st of July 2017 10:53:29 AM
Old 07-21-2017
Code:
if ($FuncrefGene !~ /exonic/i) {
                    my ($transcript) = ($GeneDetailrefGene) =~ /(?:\.\d+[+*-]|\D)(\d+)/;   # Get a numeric value if exists using (.) and (+/*/-) and capture digits into $transcript.
                             $transcript //= 0;  # Give it a value of zero if no numeric value was found.
                                $classification = 'Likely Benign' if $transcript > 10; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10

changed to:
Code:
if ($FuncrefGene !~ /exonic/i) {
                    my ($transcript) = ($GeneDetailrefGene) =~ /(?:[+*-]d=)(\d+)/;   # Get a numeric value if exists using (.) and (+/*/-) and capture digits into $transcript.
                             $transcript //= 0;  # Give it a value of zero if no numeric value was found.
                                $classification = 'Likely Benign' if $transcript > 10; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10

should capture the 43 in NM_001134408:exon3:c.415-43A>G and that wiill be the value of $transcript? I am not sure how to also use f[13} in this rule. In the cases that have multiple f[8] values, like in line 1, the first can be used.

In line 1 f[8] is

NM_001134408:exon3:c.415-43A>G;NM_001134407:exon3:c.415-43A>G;NM_000833:exon4:c.415-43A>G
 aand the ; (semi-colon) indicates the start of a new value. NM_001134408:exon3:c.415-43A>G would be the first value, so 43 is read into the $transcript variable and since f[13] is 0.0004, f[55] is VUS. Thank you Smilie.
 

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LEARN ABOUT DEBIAN

dico

DICO(1) 							   User Commands							   DICO(1)

NAME

       dico - a DICT client

SYNOPSIS

       dico [-mDSHIqatvh] [-p SERVICE] [-d NAME] [-s NAME] [-i DBNAME] [-u NAME] [-k STRING] [-c STRING] [--host=SERVER] [--port=SERVICE] [--data-
       base=NAME] [--source=ADDR]  [--match]  [--strategy=NAME]  [--levdist,  --levenshtein-distance=N]fR  [--dbs]  [--strategies]  [--serverhelp]
       [--info=DBNAME]	[--serverinfo]	[--quiet]  [--noauth]  [--sasl] [--nosasl] [--user=NAME] [--key, --passwordfR=STRING]fR [--autologin=NAME]
       [--client=STRING] [--transcript] [--verbose] [--time-stamp] [--source-info] [--help] [--usage] [--version]

DESCRIPTION

       dico is an RFC 2229 compliant dictionary client.

OPTIONS

   Server selection
       --host=SERVER
	      Connect to this server.

       -p, --port=SERVICE
	      Specify port to connect to.

       -d, --database=NAME
	      Select a database to search.

       --source=ADDR
	      Set a source address for TCP connections.

   Operation modes
       -m, --match
	      Match instead of define.

       -s, --strategy=NAME
	      Select a strategy for matching.  Implies --match.

       --levdist, --levenshtein-distance=N
	      Set maximum Levenshtein distance to N.

       -D, --dbs
	      Show available databases.

       -S, --strategies
	      Show available search strategies.

       -H, --serverhelp
	      show server help.

       -i, --info=DBNAME
	      Show information about database DBNAME.

       -I, --serverinfo
	      Show information about the server.

       -q, --quiet
	      Do not print the normal dico welcome.

   Authentication
       -a, --noauth
	      Disable authentication.

       --sasl Enable SASL authentication (default).

       --nosasl
	      Disable SASL authentication.

       -u, --user=NAME
	      Set user name for authentication.

       -k, --key, --password=STRING
	      Set shared secret for authentication.

       --autologin=NAME
	      Set the name of autologin file to use.

       -c, --client=STRING
	      Additional text for client command.

   Debugging
       -t, --transcript
	      Enable session transcript.

       -v, --verbose
	      Increase debugging verbosity level.

       --time-stamp
	      Include time stamp in the debugging output.

       --source-info
	      Include source line information in the debugging output.

   Other options
       -h, --help
	      Give this help list

       --usage
	      Give a short usage message

       --version
	      Print program version

       Mandatory or optional arguments to long options are also mandatory or optional for any corresponding short options.

REPORTING BUGS

       Report bugs to <bug-dico@gnu.org>.

COPYRIGHT

       Copyright (C) 2005, 2006, 2007, 2008 Sergey Poznyakoff License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       dicod(8),
       The full documentation for dico is maintained as a Texinfo manual.  If the info and dico-doc programs are properly installed at your  site,
       the command

	      info dico

       should give you access to the complete manual.

AUTHOR

       dico was written by Sergey Poznyakoff <gray@gnu.org.ua>.

       This manual page was written by	 (Ahmed El-Mahmoudy) <aelmahmoudy@sabily.org>, for the Debian project (and may be used by others).

dico (GNU dico 2.0)						    April 2009								   DICO(1)
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