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
paps
PAPS(1) General Commands Manual PAPS(1)NAME
paps - UTF-8 to PostScript converter using Pango
SYNOPSIS
paps [options] files...
DESCRIPTION
paps reads a UTF-8 encoded file and generates a PostScript language rendering of the file. The rendering is done by creating outline curves
through the pango ft2 backend.
OPTIONS
These programs follow the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is
included below.
--landscape
Landscape output. Default is portrait.
--columns=cl
Number of columns output. Default is 1.
Please notice this option isn't related to the terminal length as in a "80 culums terminal".
--font=desc
Set the font description. Default is Monospace 12.
--rtl Do right to left (RTL) layout.
--paper ps
Choose paper size. Known paper sizes are legal, letter and A4. Default is A4.
Postscript points
Each postscript point equals to 1/72 of an inch. 36 points are 1/2 of an inch.
--bottom-margin=bm
Set bottom margin. Default is 36 postscript points.
--top-margin=tm
Set top margin. Default is 36 postscript points.
--left-margin=lm
Set left margin. Default is 36 postscript points.
--right-margin=rm
Set right margin. Default is 36 postscript points.
--gutter-width=gw
Set gutter width. Default is 40 postscript points.
--help Show summary of options.
--header
Draw page header for each page.
--markup
Interpret the text as pango markup.
--lpi Set the lines per inch. This determines the line spacing.
--cpi Set the characters per inch. This is an alternative method of specifying the font size.
--stretch-chars
Indicates that characters should be stretched in the y-direction to fill up their vertical space. This is similar to the texttops
behaviour.
AUTHOR
paps was written by Dov Grobgeld <dov.grobgeld@gmail.com>.
This manual page was written by Lior Kaplan <kaplan@debian.org>, for the Debian project (but may be used by others).
April 17, 2006 PAPS(1)
06-05-2012
