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
file::find::object::rule::extending
File::Find::Object::Rule::Extending(3pm) User Contributed Perl Documentation File::Find::Object::Rule::Extending(3pm)NAME
File::Find::Object::Rule::Extending - the mini-guide to extending File::Find::Object::Rule
SYNOPSIS
package File::Find::Object::Rule::Random;
use strict;
use warnings;
# take useful things from File::Find::Object::Rule
use base 'File::Find::Object::Rule';
# and force our crack into the main namespace
sub File::Find::Object::Rule::random () {
my $self = shift()->_force_object;
$self->exec( sub { rand > 0.5 } );
}
1;
DESCRIPTION
File::Find::Object::Rule inherits File::Find::Rule's extensibility. It is now possibile to extend it, using the following conventions.
Declare your package
package File::Find::Object::Rule::Random;
use strict;
use warnings;
Inherit methods from File::Find::Object::Rule
# take useful things from File::Find::Object::Rule
use base 'File::Find::Object::Rule';
Force your madness into the main package
# and force our crack into the main namespace
sub File::Find::Object::Rule::random () {
my $self = shift()->_force_object;
$self->exec( sub { rand > 0.5 } );
}
Yes, we're being very cavalier here and defining things into the main File::Find::Object::Rule namespace. This is due to lack of
imaginiation on my part - I simply can't find a way for the functional and oo interface to work without doing this or some kind of
inheritance, and inheritance stops you using two File::Find::Object::Rule::Foo modules together.
For this reason try and pick distinct names for your extensions. If this becomes a problem then I may institute a semi-official registry
of taken names.
Taking no arguments.
Note the null prototype on random. This is a cheat for the procedural interface to know that your sub takes no arguments, and so allows
this to happen:
find( random => in => '.' );
If you hadn't declared "random" with a null prototype it would have consumed "in" as a parameter to it, then got all confused as it doesn't
know about a '.' rule.
NOTES ABOUT THE CALLBACK
The callback can access the File::Find::Object::Result using "$self->finder->item_obj()".
AUTHOR
Richard Clamp <richardc@unixbeard.net>
COPYRIGHT
Copyright (C) 2002 Richard Clamp. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
SEE ALSO
File::Find::Object::Rule
File::Find::::Rule::MMagic was the first extension module for File::Find::Rule, so maybe check that out.
perl v5.14.2 2012-05-05 File::Find::Object::Rule::Extending(3pm)
09-11-2017
.