<commit_before># Base class that all other mapping methods inherit from

package XrefMapper::Methods::ExonerateBasic;

use strict;
use warnings;

use File::Basename;
use IPC::Open3;

# Path to exonerate executable
#my $exonerate_path = "/usr/local/ensembl/bin/exonerate-0.9.0";
my $exonerate_path = "/rubbish/software/ensembl/bin/exonerate-1.4.0"; #  remove rubbish after wards as just to test

sub new {

  my($class, $mapper) = @_;

  my $self ={};
  bless $self,$class;
  $self->mapper($mapper);
  $self->jobcount(0);

  return $self;

}

sub mapper{
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_mapper} = $arg );
  return $self->{_mapper};
}

<commit_msg>removed old test case of incorrect exonerate path<commit_after># Base class that all other mapping methods inherit from

package XrefMapper::Methods::ExonerateBasic;

use strict;
use warnings;

use File::Basename;
use IPC::Open3;

# Path to exonerate executable
my $exonerate_path = "/usr/local/ensembl/bin/exonerate-0.9.0";

sub new {

  my($class, $mapper) = @_;

  my $self ={};
  bless $self,$class;
  $self->mapper($mapper);
  $self->jobcount(0);

  return $self;

}

sub mapper{
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_mapper} = $arg );
  return $self->{_mapper};
}


{'fraction_non_alphanumeric': 0.1633780584056827, 'fraction_numerical': 0.010260457774269928, 'mean_word_length': 4.112903225806452, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 11, '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': '4891747', 'n_tokens_mistral': 508, 'n_tokens_neox': 478, 'n_words': 118}