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Top Forums Shell Programming and Scripting How to extract data from XML file using shell scripting? Post 302843137 by Jotne on Monday 12th of August 2013 07:23:56 AM
Old 08-12-2013
Please use code tags
Give an example on what output you like to have

Lik this?
Code:
awk '{gsub(/<[^>]*>/, " ");$1=$1}1' complex.xml
PROT001 Human cytoplasmic Ensembl ENSG00000105829 UNIPROT Q12345 PROT002 Human nuclear Ensembl ENSG00000105333 UNIPROT Q14789



EDIT: Some change
Code:
awk '{gsub(/<[^>]*>/, " ");$1=$1;gsub(/PROT[0-9]/,"\n&")}1' complex.xml

PROT001 Human cytoplasmic Ensembl ENSG00000105829 UNIPROT Q12345
PROT002 Human nuclear Ensembl ENSG00000105333 UNIPROT Q14789


Last edited by Jotne; 08-12-2013 at 08:37 AM..
 

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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 2.0604 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/> AUTHOR
Moose is maintained by the Moose Cabal, along with the help of many contributors. See "CABAL" in Moose and "CONTRIBUTORS" in Moose for details. COPYRIGHT AND LICENSE
This software is copyright (c) 2012 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 v5.16.2 2012-09-19 Moose::Cookbook::Basics::Genome_OverloadingSubtypesAndCoercion(3)
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