<commit_before>=pod

=head1 NAME
	
	Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::Comparison_job_arrays

=head1 SYNOPSIS

=head1 DESCRIPTION
	Takes as input an hash of reference and non reference species DBIDs and one other key. The key is a dnafrag dbid and the values are a list of homology DBIDs ordered by their dnafrag start positions
	Proceeds to take each homolog along with a maximum of 2 neighbouring homologs each to its left and to its rights on the list.
	Used this as inputs for the next job

	Example run

	standaloneJob.pl Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::Comparison_job_arrays
=cut

package Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::Comparison_job_arrays;

use strict;
use warnings;
use Data::Dumper;

use base ('Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable');

use Bio::EnsEMBL::Registry;


=head2 param_defaults

    Description : Implements param_defaults() interface method of Bio::EnsEMBL::Hive::Process that defines module defaults for parameters. Lowest level parameters

=cut

sub param_defaults {
	return {
	    'mlss_ID'=>'20515',
		'ref_species_dbid' =>4,
        'non_ref_species_dbid' => 31,
		'chr_job'	=>	{ '36648' => [
                       '260211',
                       '70220',
                       '70250',
                       '70569',
                       '71665',
                       '287636',
                       '245625',
                       '245564',
                       '357304'
                        ]
                        },

	};
}


=head2 fetch_input

    Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.
    Here I need to retrieve the ordered chromosome ortholog hash that was data flowed here by Prepare_Per_Chr_Jobs.pm 

=cut

sub fetch_input {
#	my $self = shift;
#	$self->param('mlss_ID', $self->param_required('mlss_ID'));
#	my $chr_job = $self->param_required('ortholog_info_hashref');
#	print "##############################\n\n";
#	print Dumper($chr_job);
#	print "##############################\n\n";
#	$self->param('chr_job')
}


sub run {<commit_msg>made some changes to hard coded example inputs<commit_after>=pod

=head1 NAME
	
	Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::Comparison_job_arrays

=head1 SYNOPSIS

=head1 DESCRIPTION
	Takes as input an hash of reference and non reference species DBIDs and one other key. The key is a dnafrag dbid and the values are a list of homology DBIDs ordered by their dnafrag start positions
	Proceeds to take each homolog along with a maximum of 2 neighbouring homologs each to its left and to its rights on the list.
	Used this as inputs for the next job

	Example run

	standaloneJob.pl Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::Comparison_job_arrays
=cut

package Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::Comparison_job_arrays;

use strict;
use warnings;
use Data::Dumper;

use base ('Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable');

use Bio::EnsEMBL::Registry;


=head2 param_defaults

    Description : Implements param_defaults() interface method of Bio::EnsEMBL::Hive::Process that defines module defaults for parameters. Lowest level parameters

=cut

sub param_defaults {
	return {
	    'mlss_ID'=>'100021',
		'ref_species_dbid' =>155,
        'non_ref_species_dbid' => 31,
		'chr_job'	=>	{ '14026395' => [
                          '14803',
                          '14469',
                          '46043'
                        ]
                        },

	};
}


=head2 fetch_input

    Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.
    Here I need to retrieve the ordered chromosome ortholog hash that was data flowed here by Prepare_Per_Chr_Jobs.pm 

=cut

sub fetch_input {
#	my $self = shift;
#	$self->param('mlss_ID', $self->param_required('mlss_ID'));
#	my $chr_job = $self->param_required('ortholog_info_hashref');
#	print "##############################\n\n";
#	print Dumper($chr_job);
#	print "##############################\n\n";
#	$self->param('chr_job')
}


sub run {
{'fraction_non_alphanumeric': 0.1264173703256936, 'fraction_numerical': 0.026296743063932447, 'mean_word_length': 3.314255983350676, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 21, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1091016', 'n_tokens_mistral': 1430, 'n_tokens_neox': 1264, 'n_words': 379}