changed to:
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 .
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::rule::extending
File::Find::Rule::Extending(3pm) User Contributed Perl Documentation File::Find::Rule::Extending(3pm)NAME
File::Find::Rule::Extending - the mini-guide to extending File::Find::Rule
SYNOPSIS
package File::Find::Rule::Random;
use strict;
# take useful things from File::Find::Rule
use base 'File::Find::Rule';
# and force our crack into the main namespace
sub File::Find::Rule::random () {
my $self = shift()->_force_object;
$self->exec( sub { rand > 0.5 } );
}
1;
DESCRIPTION
File::Find::Rule went down so well with the buying public that everyone wanted to add extra features. With the 0.07 release this became a
possibility, using the following conventions.
Declare your package
package File::Find::Rule::Random;
use strict;
Inherit methods from File::Find::Rule
# take useful things from File::Find::Rule
use base 'File::Find::Rule';
Force your madness into the main package
# and force our crack into the main namespace
sub File::Find::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::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::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.
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::Rule
File::Find::Rule::MMagic was the first extension module, so maybe check that out.
perl v5.12.4 2011-09-19 File::Find::Rule::Extending(3pm)