I am not exactly sure I follow but that's ok. Fortunately for us, I do not have to understand genome reference indexes or alleles for that matter to understand logic.
Using the example I have given you, you should be able see that while I set $ref as a static value (A), you can follow the exact logic inside the while loop to pull a value or array of values from another file. If all needed values exist in "THIS" file, then I have already given you what you need.
these lines do something very nice for you, namely it grabs all text and splits it into separate variables delimiting on white space (or multiple white space) characters.All text surrounded in parenthesis are "kept".
You can see that I have given friendly names to the index and genotype columns, but $2 would contain the "Chr" column and $4 would contain the "Mutation Type" column with that regex match. You can easily give them friendly names to reuse as well...
Going a bit further, if you need to split geno into 2 separate characters you can now take the $geno variable and do something like this:
Example:
Code:
my ($geno1,$geno2) = split(undef,$geno);
The framework is all here, for you to do everything you want now, but for me (or others) to give you a better solution it would require a more logical approach in explaining the problem I fear.
Maybe I am slow, but I do not see (based on your explanation) the correlation you are trying to make with these references/alleles.
You say:
Quote:
In index 3 and 4, however, the reference alleles are 'C' and 'G' respectively, and and both of these cases, the coordinating genotype does not have an allele that matches the reference.
What is considered a "coordinating genotype?
What are the reference alleles?
Last letter in the pair of 2 is reference?
More precisely it would be easier to phrase as:
The second letter in that column must match the first.
Hello all
im facing some kind of problem i have this string :
functionA() $" "$ functionB("arg1") $" = "$
i will like to replace all the pairs of opening and closing "$" to be something like that
functionA() <#" "#> functionB("arg1") <#" = "#>
i cant of course do is with simple ... (1 Reply)
Hi.
I have three arrays.
@a=('AB','CD','EF');
@b=('AB,'DG',HK');
@c=('DD','TT','MM');
I want to compare the elements of the first two array and if they match then so some substition.
I tried using the if statement using the scalar value of the array but its not giving me any output.
... (7 Replies)
Hi all,
I am trying to compare two arrays in perl using the following code.
foreach $item (@arrayA){
push(@arrayC, $item) unless grep(/$item/, @arrayB); ... (1 Reply)
I have a main file with variable tokens like this:
name: File1
===========
Destination/Company=@deploy.company@
Destination/Environment=@deploy.env@
Destination/Location=@deploy.location@
Destination/Domain=@deploy.location@
MIG_GatewayAddresses=@deploy.gwaddress@
MIG_URL=@deploy.mig_url@... (1 Reply)
Hi there, i have been trying different methods and i wonder if somebody could explain to me how i would perform a comparison on two arrays for example
my @array1 = ("gary" ,"peter", "paul");
my @array2 = ("gary" ,"peter", "joe");
I have two arrays above, and i want to something like this... (5 Replies)
Hi,
I'm new to perl and i have to write a perl script that will compare to log/txt files and display the differences. Unfortunately I'm not allowed to use any complied binaries or applications like diff or comm.
So far i've across a code like this:
use strict;
use warnings;
my $list1;... (2 Replies)
What do i need to do have the below perl program load 205 million record files into the hash. It currently works on smaller files, but not working on huge files. Any idea what i need to do to modify to make it work with huge files:
#!/usr/bin/perl
$ot1=$ARGV;
$ot2=$ARGV;
open(mfileot1,... (12 Replies)
I have these two file that I am trying to compare using shell arrays. I need to find out the changed or the missing
enteries from File2. For example. The line "f nsd1" in file2 is different from file1 and the line "g nsd6" is missing
from file2.
I dont want to use "for loop" because my files... (2 Replies)
Hi everyone
I have a question for you, as I am trying to learn more about Perl and work with some weather data. I have an ascii file (shown below) that has 10 lines with different columns. What I would like is have Perl find an "anomalous" value by comparing a field with the values from the last... (2 Replies)
Discussion started by: lucshi09
2 Replies
LEARN ABOUT DEBIAN
devel::findref
FindRef(3pm) User Contributed Perl Documentation FindRef(3pm)NAME
Devel::FindRef - where is that reference to my variable hiding?
SYNOPSIS
use Devel::FindRef;
print Devel::FindRef::track $some_variable;
DESCRIPTION
Tracking down reference problems (e.g. you expect some object to be destroyed, but there are still references to it that keep it alive) can
be very hard. Fortunately, perl keeps track of all its values, so tracking references "backwards" is usually possible.
The "track" function can help track down some of those references back to the variables containing them.
For example, for this fragment:
package Test;
use Devel::FindRef;
use Scalar::Util;
our $var = "hi
";
my $global_my = $var;
our %global_hash = (ukukey => $var);
our $global_hashref = { ukukey2 => $var };
sub testsub {
my $testsub_local = $global_hashref;
print Devel::FindRef::track $var;
}
my $closure = sub {
my $closure_var = $_[0];
Scalar::Util::weaken (my $weak_ref = $var);
testsub;
};
$closure->($var);
The output is as follows (or similar to this, in case I forget to update the manpage after some changes):
SCALAR(0x7cc888) [refcount 6] is
+- referenced by REF(0x8abcc8) [refcount 1], which is
| in the lexical '$closure_var' in CODE(0x8abc50) [refcount 4], which is
| +- the closure created at tst:18.
| +- referenced by REF(0x7d3c58) [refcount 1], which is
| | in the lexical '$closure' in CODE(0x7ae530) [refcount 2], which is
| | +- the containing scope for CODE(0x8ab430) [refcount 3], which is
| | | in the global &Test::testsub.
| | +- the main body of the program.
| +- in the lexical '&' in CODE(0x7ae530) [refcount 2], which was seen before.
+- referenced by REF(0x7cc7c8) [refcount 1], which is
| in the lexical '$global_my' in CODE(0x7ae530) [refcount 2], which was seen before.
+- in the global $Test::var.
+- referenced by REF(0x7cc558) [refcount 1], which is
| in the member 'ukukey2' of HASH(0x7ae140) [refcount 2], which is
| +- referenced by REF(0x8abad0) [refcount 1], which is
| | in the lexical '$testsub_local' in CODE(0x8ab430) [refcount 3], which was seen before.
| +- referenced by REF(0x8ab4f0) [refcount 1], which is
| in the global $Test::global_hashref.
+- referenced by REF(0x7ae518) [refcount 1], which is
| in the member 'ukukey' of HASH(0x7d3bb0) [refcount 1], which is
| in the global %Test::global_hash.
+- referenced by REF(0x7ae2f0) [refcount 1], which is
a temporary on the stack.
It is a bit convoluted to read, but basically it says that the value stored in $var is referenced by:
- the lexical $closure_var(0x8abcc8), which is inside an instantiated closure, which in turn is used quite a bit.
- the package-level lexical $global_my.
- the global package variable named $Test::var.
- the hash element "ukukey2", in the hash in the my variable $testsub_local in the sub "Test::testsub" and also in the hash "$referenced by
Test::hash2".
- the hash element with key "ukukey" in the hash stored in %Test::hash.
- some anonymous mortalised reference on the stack (which is caused by calling "track" with the expression "$var", which creates the
reference).
And all these account for six reference counts.
EXPORTS
None.
FUNCTIONS
$string = Devel::FindRef::track $ref[, $depth]
Track the perl value pointed to by $ref up to a depth of $depth and return a descriptive string. $ref can point at any perl value, be
it anonymous sub, hash, array, scalar etc.
This is the function you most often use.
@references = Devel::FindRef::find $ref
Return arrayrefs that contain [$message, $ref] pairs. The message describes what kind of reference was found and the $ref is the
reference itself, which can be omitted if "find" decided to end the search. The returned references are all weak references.
The "track" function uses this to find references to the value you are interested in and recurses on the returned references.
$ref = Devel::FindRef::ptr2ref $integer
Sometimes you know (from debugging output) the address of a perl scalar you are interested in (e.g. "HASH(0x176ff70)"). This function
can be used to turn the address into a reference to that scalar. It is quite safe to call on valid addresses, but extremely dangerous
to call on invalid ones.
# we know that HASH(0x176ff70) exists, so turn it into a hashref:
my $ref_to_hash = Devel::FindRef::ptr2ref 0x176ff70;
$ref = Devel::FindRef::ref2ptr $reference
The opposite of "ptr2ref", above: returns the internal address of the value pointed to by the passed reference. No checks whatsoever
will be done, so don't use this.
ENVIRONMENT VARIABLES
You can set the environment variable "PERL_DEVEL_FINDREF_DEPTH" to an integer to override the default depth in "track". If a call
explicitly specified a depth it is not overridden.
AUTHOR
Marc Lehmann <pcg@goof.com>.
COPYRIGHT AND LICENSE
Copyright (C) 2007, 2008 by Marc Lehmann.
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.8 or,
at your option, any later version of Perl 5 you may have available.
perl v5.14.2 2009-08-30 FindRef(3pm)
06-05-2012
