<commit_before>package EnsEMBL::Web::UserConfig::TSV_sampletranscript;
use strict;
use EnsEMBL::Web::UserConfig;
use vars qw(@ISA);
@ISA = qw(EnsEMBL::Web::UserConfig);

sub init {
  my ($self) = @_;
  $self->{'_userdatatype_ID'} = 36;
  $self->{'_transcript_names_'} = 'yes';
  $self->{'_add_labels' }  = 1;

  $self->{'general'}->{'TSV_sampletranscript'} = {
    '_artefacts' => [qw(coverage_top TSV_transcript TSV_snps cxoverage_bottom)],#GSV_pfam GSV_prints GSV_prosite GSV_pfscan)],
    '_options'  => [qw(pos col known unknown)],
    '_settings' => {
      'opt_pdf' => 0, 'opt_svg' => 0, 'opt_postscript' => 0,
      'opt_zclick'     => 1,
      'show_labels' => 'no',
      'context'   => 100,
      'width'   => 900,
      'bgcolor'   => 'background1',
      'bgcolour1' => 'background1',
      'bgcolour2' => 'background1',

      'validation' => [
        [ 'opt_freq'       => 'By frequency' ],
        [ 'opt_cluster'    => 'By cluster' ],
        [ 'opt_doublehit'  => 'By doublehit' ],
        [ 'opt_submitter'  => 'By submitter' ],
        [ 'opt_hapmap'     => 'Hapmap' ],
        [ 'opt_noinfo'     => 'No information' ],
      ],
      'classes' => [
        [ 'opt_in-del'   => 'In-dels' ],
        [ 'opt_snp'      => 'SNPs' ],
        [ 'opt_mixed'    => 'Mixed variations' ],
        [ 'opt_microsat' => 'Micro-satellite repeats' ],
        [ 'opt_named'    => 'Named variations' ],
        [ 'opt_mnp'      => 'MNPs' ],
        [ 'opt_het'      => 'Hetrozygous variations' ],
        [ 'opt_'         => 'Unclassified' ],
      ],
      'types' => [
        [ 'opt_stop_lost',            => 'Stop lost' ],
        [ 'opt_stop_gained',          => 'Stop gained' ],
        [ 'opt_frameshift_coding'     => 'Coding variations' ],
        [ 'opt_non_synonymous_coding' => 'Non-synonymous SNPs' ],
        [ 'opt_essential_splice_site' => 'Essential splice site' ],
        [ 'opt_splice_site'           => 'Splice site' ],
        [ 'opt_regulatory_region',    => 'Regulatory region variations' ],
        [ 'opt_synonymous_coding'     => 'Synonymous SNPs' ],
        [ 'opt_5prime_utr'            => "5' UTR vatiations" ],
        [ 'opt_3prime_utr'            => "3' UTR vatiations" ],
        [ 'opt_downstream'            => 'Downstream variations' ],<commit_msg>added source menu to GSV. Ordered the SNP Types differently. Added 'missing' track to GSV. Added snp class unclassified to GSV<commit_after>package EnsEMBL::Web::UserConfig::TSV_sampletranscript;
use strict;
use EnsEMBL::Web::UserConfig;
use vars qw(@ISA);
@ISA = qw(EnsEMBL::Web::UserConfig);

sub init {
  my ($self) = @_;
  $self->{'_userdatatype_ID'} = 36;
  $self->{'_transcript_names_'} = 'yes';
  $self->{'_add_labels' }  = 1;

  $self->{'general'}->{'TSV_sampletranscript'} = {
    '_artefacts' => [qw(coverage_top TSV_transcript TSV_snps cxoverage_bottom)],#GSV_pfam GSV_prints GSV_prosite GSV_pfscan)],
    '_options'  => [qw(pos col known unknown)],
    '_settings' => {
      'opt_pdf' => 0, 'opt_svg' => 0, 'opt_postscript' => 0,
      'opt_zclick'     => 1,
      'show_labels' => 'no',
      'context'   => 100,
      'width'   => 900,
      'bgcolor'   => 'background1',
      'bgcolour1' => 'background1',
      'bgcolour2' => 'background1',

      'validation' => [
        [ 'opt_freq'       => 'By frequency' ],
        [ 'opt_cluster'    => 'By cluster' ],
        [ 'opt_doublehit'  => 'By doublehit' ],
        [ 'opt_submitter'  => 'By submitter' ],
        [ 'opt_hapmap'     => 'Hapmap' ],
        [ 'opt_noinfo'     => 'No information' ],
      ],
      'classes' => [
        [ 'opt_in-del'   => 'In-dels' ],
        [ 'opt_snp'      => 'SNPs' ],
        [ 'opt_mixed'    => 'Mixed variations' ],
        [ 'opt_microsat' => 'Micro-satellite repeats' ],
        [ 'opt_named'    => 'Named variations' ],
        [ 'opt_mnp'      => 'MNPs' ],
        [ 'opt_het'      => 'Hetrozygous variations' ],
        [ 'opt_'         => 'Unclassified' ],
      ],
      'types' => [
        [ 'opt_stop_lost',            => 'Stop lost' ],
        [ 'opt_stop_gained',          => 'Stop gained' ],
        [ 'opt_frameshift_coding'     => 'Coding variations' ],
        [ 'opt_non_synonymous_coding' => 'Non-synonymous SNPs' ],
        [ 'opt_essential_splice_site' => 'Essential splice site' ],
        [ 'opt_splice_site'           => 'Splice site' ],
        [ 'opt_regulatory_region',    => 'Regulatory region variations' ],
        [ 'opt_synonymous_coding'     => 'Synonymous SNPs' ],
        [ 'opt_5prime_utr'            => "5' UTR variations" ],
        [ 'opt_3prime_utr'            => "3' UTR variations" ],
        [ 'opt_downstream'            => 'Downstream variations' ],
{'fraction_non_alphanumeric': 0.17927947132807504, 'fraction_numerical': 0.009379663184822, 'mean_word_length': 2.356223175965665, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 95, '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': '4149361', 'n_tokens_mistral': 1740, 'n_tokens_neox': 1631, 'n_words': 286}