<commit_before>package CoGe::Builder::Tools::SynMap3D;

use Moose;

use CoGe::Accessory::Jex;
use CoGe::Accessory::Web qw( get_defaults );
use CoGe::Accessory::Workflow;
use CoGe::Accessory::Utils qw(units);
use CoGe::Builder::CommonTasks qw( create_gff_generation_job );
use CoGe::Builder::Tools::SynMap qw( add_jobs defaults );
use CoGe::Core::Storage qw( get_workflow_paths );
use Data::Dumper;
#use File::Path qw(mkpath);
use File::Spec::Functions;
use JSON qw( encode_json );
use POSIX;

sub build {
	my $self = shift;
	my $xid = $self->params->{genome_id1};
	my $yid = $self->params->{genome_id2};
	my $zid = $self->params->{genome_id3};
	my ($dir1, $dir2) = sort($xid, $yid);
	my ($dir3, $dir4) = sort($xid, $zid);
	my ($dir5, $dir6) = sort($yid, $zid);

	my $SYN3DIR = $self->conf->{SYN3DIR};
	my $SCRIPTDIR = catdir( $self->conf->{SCRIPTDIR}, 'synmap' );
	my $PYTHON = $self->conf->{PYTHON}

	my $MERGER = 'nice ' . $PYTHON . ' ' . catfile($SCRIPTDIR, 'synmerge_3.py');

	#########################################################################
	# Add SynMap jobs.
	#########################################################################
	my @genome_ids;
	my $i = 1;
	while (1) {
		if ($self->params->{'genome_id' . $i}) {
			push @genome_ids, $self->params->{'genome_id' . $i++};
		}
		else {
			last;
		}
	}
	for (my $j=1; $j<$i-1; $j++) {
		for (my $k=$j+1; $k<$i; $k++) {<commit_msg>Fix syntax error<commit_after>package CoGe::Builder::Tools::SynMap3D;

use Moose;

use CoGe::Accessory::Jex;
use CoGe::Accessory::Web qw( get_defaults );
use CoGe::Accessory::Workflow;
use CoGe::Accessory::Utils qw(units);
use CoGe::Builder::CommonTasks qw( create_gff_generation_job );
use CoGe::Builder::Tools::SynMap qw( add_jobs defaults );
use CoGe::Core::Storage qw( get_workflow_paths );
use Data::Dumper;
#use File::Path qw(mkpath);
use File::Spec::Functions;
use JSON qw( encode_json );
use POSIX;

sub build {
	my $self = shift;
	my $xid = $self->params->{genome_id1};
	my $yid = $self->params->{genome_id2};
	my $zid = $self->params->{genome_id3};
	my ($dir1, $dir2) = sort($xid, $yid);
	my ($dir3, $dir4) = sort($xid, $zid);
	my ($dir5, $dir6) = sort($yid, $zid);

	my $SYN3DIR = $self->conf->{SYN3DIR};
	my $SCRIPTDIR = catdir( $self->conf->{SCRIPTDIR}, 'synmap' );
	my $PYTHON = $self->conf->{PYTHON};

	my $MERGER = 'nice ' . $PYTHON . ' ' . catfile($SCRIPTDIR, 'synmerge_3.py');

	#########################################################################
	# Add SynMap jobs.
	#########################################################################
	my @genome_ids;
	my $i = 1;
	while (1) {
		if ($self->params->{'genome_id' . $i}) {
			push @genome_ids, $self->params->{'genome_id' . $i++};
		}
		else {
			last;
		}
	}
	for (my $j=1; $j<$i-1; $j++) {
		for (my $k=$j+1; $k<$i; $k++) {
{'fraction_non_alphanumeric': 0.2987152034261242, 'fraction_numerical': 0.01284796573875803, 'mean_word_length': 5.38496583143508, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 35, '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': '5102477', 'n_tokens_mistral': 1175, 'n_tokens_neox': 1120, 'n_words': 234}