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Top Forums Shell Programming and Scripting User input and run awk using the input Post 302967336 by sea on Tuesday 23rd of February 2016 01:42:52 AM
Old 02-23-2016
This:
Code:
printf "Please enter the gene(s) of interest, use a comma between multiple: "
IFS="," read -a gene
        printf "the indicated genes will now be loaded and used to calculate coverage\n"

Will not work as you expect.

In fact, you tell to only catch the first genom only, and no other.
Because you say the IFS shall be ',' which is shall be used to seperate the genoms, mainwhile, you only read 1 genom, as 'gene' will be split into as many arguments/variables as the user passes using ','.

Saying:
Replcae the IFS= part to a later procedure, when parsing the user input.
Parsing is done after reading, or if while reading, it must be a limited (say pass 3 genoms, then you mus tread 3 variables - not just one).

I'm no scientist, but afaik a genom doesnt have 'spaces' in between, so they might just seperate the genoms passed by spaces OR coma - since the IFS is removed, that doesnt matter, in fact, its even simpler to work with the passed genoms, if the users do not use ',' to seperate the list.

Only use the red parts if you insist of using coma to seperate the list, if using space its not required at all.
Code:
read genes
oIFS="$IFS"
IFS=","
for gene in $genes;do
	echo "Working with genom: $gene"
done
IFS="$oIFS"

Other than that, please make the according corrections of for loops as Don already stated.

Thank you and hope this helps
This User Gave Thanks to sea For This Post:
 

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Moose::Cookbook::Basics::Genome_OverloadingSubtypesAndCoUseroContributed Perl DocMoose::Cookbook::Basics::Genome_OverloadingSubtypesAndCoercion(3)

NAME
Moose::Cookbook::Basics::Genome_OverloadingSubtypesAndCoercion - Operator overloading, subtypes, and coercion VERSION
version 2.1202 SYNOPSIS
package Human; use Moose; use Moose::Util::TypeConstraints; subtype 'Sex' => as 'Str' => where { $_ =~ m{^[mf]$}s }; has 'sex' => ( is => 'ro', isa => 'Sex', required => 1 ); has 'mother' => ( is => 'ro', isa => 'Human' ); has 'father' => ( is => 'ro', isa => 'Human' ); use overload '+' => &_overload_add, fallback => 1; sub _overload_add { my ( $one, $two ) = @_; die('Only male and female humans may create children') if ( $one->sex() eq $two->sex() ); my ( $mother, $father ) = ( $one->sex eq 'f' ? ( $one, $two ) : ( $two, $one ) ); my $sex = 'f'; $sex = 'm' if ( rand() >= 0.5 ); return Human->new( sex => $sex, mother => $mother, father => $father, ); } DESCRIPTION
This Moose cookbook recipe shows how operator overloading, coercion, and subtypes can be used to mimic the human reproductive system (well, the selection of genes at least). INTRODUCTION
Our "Human" class uses operator overloading to allow us to "add" two humans together and produce a child. Our implementation does require that the two objects be of opposite sex. Remember, we're talking about biological reproduction, not marriage. While this example works as-is, we can take it a lot further by adding genes into the mix. We'll add the two genes that control eye color, and use overloading to combine the genes from the parent to model the biology. What is Operator Overloading? Overloading is not a Moose-specific feature. It's a general OO concept that is implemented in Perl with the "overload" pragma. Overloading lets objects do something sane when used with Perl's built in operators, like addition ("+") or when used as a string. In this example we overload addition so we can write code like "$child = $mother + $father". GENES
There are many genes which affect eye color, but there are two which are most important, gey and bey2. We will start by making a class for each gene. Human::Gene::bey2 package Human::Gene::bey2; use Moose; use Moose::Util::TypeConstraints; type 'bey2_color' => where { $_ =~ m{^(?:brown|blue)$} }; has 'color' => ( is => 'ro', isa => 'bey2_color' ); This class is trivial. We have a type constraint for the allowed colors, and a "color" attribute. Human::Gene::gey package Human::Gene::gey; use Moose; use Moose::Util::TypeConstraints; type 'gey_color' => where { $_ =~ m{^(?:green|blue)$} }; has 'color' => ( is => 'ro', isa => 'gey_color' ); This is nearly identical to the "Humane::Gene::bey2" class, except that the gey gene allows for different colors. EYE COLOR
We could just give four attributes (two of each gene) to the "Human" class, but this is a bit messy. Instead, we'll abstract the genes into a container class, "Human::EyeColor". Then a "Human" can have a single "eye_color" attribute. package Human::EyeColor; use Moose; use Moose::Util::TypeConstraints; coerce 'Human::Gene::bey2' => from 'Str' => via { Human::Gene::bey2->new( color => $_ ) }; coerce 'Human::Gene::gey' => from 'Str' => via { Human::Gene::gey->new( color => $_ ) }; has [qw( bey2_1 bey2_2 )] => ( is => 'ro', isa => 'Human::Gene::bey2', coerce => 1 ); has [qw( gey_1 gey_2 )] => ( is => 'ro', isa => 'Human::Gene::gey', coerce => 1 ); The eye color class has two of each type of gene. We've also created a coercion for each class that coerces a string into a new object. Note that a coercion will fail if it attempts to coerce a string like "indigo", because that is not a valid color for either type of gene. As an aside, you can see that we can define several identical attributes at once by supplying an array reference of names as the first argument to "has". We also need a method to calculate the actual eye color that results from a set of genes. The bey2 brown gene is dominant over both blue and green. The gey green gene is dominant over blue. sub color { my ($self) = @_; return 'brown' if ( $self->bey2_1->color() eq 'brown' or $self->bey2_2->color() eq 'brown' ); return 'green' if ( $self->gey_1->color() eq 'green' or $self->gey_2->color() eq 'green' ); return 'blue'; } We'd like to be able to treat a "Human::EyeColor" object as a string, so we define a string overloading for the class: use overload '""' => &color, fallback => 1; Finally, we need to define overloading for addition. That way we can add together two "Human::EyeColor" objects and get a new one with a new (genetically correct) eye color. use overload '+' => &_overload_add, fallback => 1; sub _overload_add { my ( $one, $two ) = @_; my $one_bey2 = 'bey2_' . _rand2(); my $two_bey2 = 'bey2_' . _rand2(); my $one_gey = 'gey_' . _rand2(); my $two_gey = 'gey_' . _rand2(); return Human::EyeColor->new( bey2_1 => $one->$one_bey2->color(), bey2_2 => $two->$two_bey2->color(), gey_1 => $one->$one_gey->color(), gey_2 => $two->$two_gey->color(), ); } sub _rand2 { return 1 + int( rand(2) ); } When two eye color objects are added together, the "_overload_add()" method will be passed two "Human::EyeColor" objects. These are the left and right side operands for the "+" operator. This method returns a new "Human::EyeColor" object. ADDING EYE COLOR TO ";Human"s Our original "Human" class requires just a few changes to incorporate our new "Human::EyeColor" class. use List::MoreUtils qw( zip ); coerce 'Human::EyeColor' => from 'ArrayRef' => via { my @genes = qw( bey2_1 bey2_2 gey_1 gey_2 ); return Human::EyeColor->new( zip( @genes, @{$_} ) ); }; has 'eye_color' => ( is => 'ro', isa => 'Human::EyeColor', coerce => 1, required => 1, ); We also need to modify "_overload_add()" in the "Human" class to account for eye color: return Human->new( sex => $sex, eye_color => ( $one->eye_color() + $two->eye_color() ), mother => $mother, father => $father, ); CONCLUSION
The three techniques we used, overloading, subtypes, and coercion, combine to provide a powerful interface. If you'd like to learn more about overloading, please read the documentation for the overload pragma. To see all the code we created together, take a look at t/recipes/basics_recipe9.t. NEXT STEPS
Had this been a real project we'd probably want: Better Randomization with Crypt::Random Characteristic Base Class Mutating Genes More Characteristics Artificial Life LICENSE
This work is licensed under a Creative Commons Attribution 3.0 Unported License. License details are at: <http://creativecommons.org/licenses/by/3.0/> AUTHORS
o Stevan Little <stevan.little@iinteractive.com> o Dave Rolsky <autarch@urth.org> o Jesse Luehrs <doy@tozt.net> o Shawn M Moore <code@sartak.org> o XXXX XXX'XX (Yuval Kogman) <nothingmuch@woobling.org> o Karen Etheridge <ether@cpan.org> o Florian Ragwitz <rafl@debian.org> o Hans Dieter Pearcey <hdp@weftsoar.net> o Chris Prather <chris@prather.org> o Matt S Trout <mst@shadowcat.co.uk> COPYRIGHT AND LICENSE
This software is copyright (c) 2006 by Infinity Interactive, Inc.. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. perl v5.18.2 2014-01-19 Moose::Cookbook::Basics::Genome_OverloadingSubtypesAndCoercion(3)
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