I think the below will capture lines 2-6, but not line 1 (looks like 018328) is being captured by the regex. Is the syntax correct or is there a better way? Thank you .
perl
Code:
if ($FuncrefGene !~ /exonic/i && $GeneDetailrefGene=~/\D(\d+)/) { # capture the digits into $1
if ($1 > 11) { #
$1 ||= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign'; # Reclassify intronic variants (with distance only) based on distance to exon > 10 to Likely Benign
}
}
else {
if ($FuncrefGene !~ /exonic/i && $GeneDetailrefGene=~/(\D\d+)/) { # capture the digits after any non-digit into $1
if ($1 > 11) { #
$1 ||= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign'; # Reclassify intronic variants (with distance only) based on distance to exon > 10 to Likely Benign
}
}
else {
if ($FuncrefGene !~ /exonic/i) {
my ($transcript) = ($GeneDetailrefGene) =~ /(?:\.\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 > 11; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10
}
}
Hi
i am new to scripting. i have a file file.dat with content as :
CONTENT_STORAGE PERCENTAGE FLAG:
/storage_01 64% 0
/storage_02 17% 1
I need to update the value of FLAG for a particular CONTENT_STORAGE value
I have written the following code
#!/bin/sh
threshold=20... (1 Reply)
I have a text file like this:
subject1:LecturerA:10
subject2:LecturerA:40
if I was given string in column 1 and 2 (which are subject 1 and LecturerA) , i need to update 3rd field of that line containing that given string , which is, number 10 need to be updated to 100 ,for example.
The... (6 Replies)
I am trying to add a condition to the below perl that will capture the GTtag and place a specific string in the last field of each line. The problem is that the GT value used is not right after the tag rather it is a few fields away. The values should always be 0/1 or 1/2 and are in bold in the... (12 Replies)
In the tab-delimeted input file below I am trying to use awk to update the value in $2 if TYPE=ins in bold, by adding the value of
HRUN= in italics. In the below since in line 1 TYPE=ins the 117282541 value in $2 has 6 added because that is the value of HRUN=.
Hopefully the awk is a start but I... (2 Replies)
In the perl below I am trying to set/update the value of $14 (last field) in file2, using the matching NM_ in $12
or $9 in file2 with the NM_ in $2 of file1.
The lengths of $9 and $12 can be variable but what is consistent is the start pattern will always be NM_ and the end pattern is always
;... (4 Replies)
In the perl there is a default rule that sets f to VUS, and then a seris of rules that will change f based on the result that is
obtained from the rule. The code below is a rule that is supposed to be applicable to lines 2-4 because this rule just looks at the digit in f. So in line 2 f is 27... (4 Replies)
I have been reading old posts and trying to come up with a solution for the below: Use a tab-delimited input file to assign
point to variables that are used to update a specific field, Rank. I really couldn't find too much in the way of assigning points
to variable, but made an attempt at an awk... (4 Replies)
I have an input file with
A=xyz
B=pqr
I would want the value in Second Field (xyz or pqr) updated with a value present in Shell Variable based on the value passed in the first field. (A or B )
while read line
do
NEW_VALUE = `some functionality done on $line`
If $line=First Field-... (1 Reply)
Hi,
So awk is driving me crazy on this one. I have searched everywhere and read man, docs and every related post Google can find and still no luck. The actual files I need to run this on are sensitive in nature, but it is the same thing as if I needed to calculate weighted grades for multiple... (15 Replies)
Discussion started by: cotilloe
15 Replies
LEARN ABOUT DEBIAN
dicod
DICOD(8) System Administration Utilities DICOD(8)NAME
dicod - a DICT daemon
SYNOPSIS
dicod [-fEsiTth] [-I DIR] [-x LEVEL-SPEC] [--config=FILE] [--foreground] [--stderr] [--syslog] [--preprocessor=PROG] [--no-preprocessor]
[--include-dir=DIR] [--single-process] [--inetd] [--transcript] [--no-transcript] [--debug=LEVEL-SPEC] [--source-info] [--trace-grammar]
[--trace-lex] [--config-help] [--lint] [--help] [--usage] [--version]
DESCRIPTION
dicod is an implementation of DICT server (RFC 2229). It is fully modular: the daemon itself (dicod) provides only the server functional-
ity, but it knows nothing about database formats. Actual searches are performed by functions supplied in loadable modules. A single module
can serve one or more databases.
OPTIONS --config=FILE
Read this configuration file.
-f, --foreground
Operate in foreground.
--stderr
Output diagnostic to stderr.
--syslog
Output diagnostic to syslog (default).
-E Preprocess configuration file and exit
--preprocessor=PROG
Use PROG as a preprocessor for config file.
--no-preprocessor
Do not use external preprocessor.
-I, --include-dir=DIR
Add the directory DIR to the list of directories to be searched for preprocessor include files
-s, --single-process
Single-process mode.
-i, --inetd
Inetd mode.
-T, --transcript
Enable session transcript.
--no-transcript
Disable session transcript.
-x, --debug=LEVEL-SPEC
Set debug verbosity level.
--source-info
Include source line information in the debugging output.
--trace-grammar
Trace parsing of configuration file.
--trace-lex
Trace config file lexer.
--config-help
Show configuration file summary.
-t, --lint
Check configuration file syntax and exit.
-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 dico(1),
The full documentation for dicod is maintained as a Texinfo manual. If the info and dico-doc programs are properly installed at your site,
the command
info dicod
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).
dicod (GNU dico 2.0) April 2009 DICOD(8)
09-11-2017
.