<commit_before>=head1 LICENSE

 Copyright (c) 1999-2013 The European Bioinformatics Institute and
 Genome Research Limited.  All rights reserved.

 This software is distributed under a modified Apache license.
 For license details, please see

   http://www.ensembl.org/info/about/legal/code_licence.html

=head1 CONTACT

 Please email comments or questions to the public Ensembl
 developers list at <<EMAIL>>.

 Questions may also be sent to the Ensembl help desk at
 <<EMAIL>>.

=cut

=head1 NAME

Bio::EnsEMBL::Variation::TranscriptVariation

=head1 SYNOPSIS

    use Bio::EnsEMBL::Variation::TranscriptVariation;

    my $tv = Bio::EnsEMBL::Variation::TranscriptVariation->new(
        -transcript        => $transcript,
        -variation_feature => $var_feat
    );

    print "consequence type: ", (join ",", @{$tv->consequence_type}), "\n";
    print "cdna coords: ", $tv->cdna_start, '-', $tv->cdna_end, "\n";
    print "cds coords: ", $tv->cds_start, '-', $tv->cds_end, "\n";
    print "pep coords: ", $tv->translation_start, '-',$tv->translation_end, "\n";
    print "amino acid change: ", $tv->pep_allele_string, "\n";
    print "codon change: ", $tv->codons, "\n";
    print "allele sequences: ", (join ",", map { $_->variation_feature_seq } 
        @{ $tv->get_all_TranscriptVariationAlleles }, "\n";

=head1 DESCRIPTION

A TranscriptVariation object represents a variation feature which is in close
proximity to an Ensembl transcript. A TranscriptVariation object has several
attributes which define the relationship of the variation to the transcript.

=cut

package Bio::EnsEMBL::Variation::TranscriptVariation;

use strict;
use warnings;

use Bio::EnsEMBL::Utils::Scalar qw(assert_ref check_ref);
use Bio::EnsEMBL::Variation::TranscriptVariationAllele;
use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(overlap within_cds);
use Bio::EnsEMBL::Variation::BaseTranscriptVariation;

use base qw(Bio::EnsEMBL::Variation::BaseTranscriptVariation Bio::EnsEMBL::Variation::VariationFeatureOverlap);

=head2 new

  Arg [-TRANSCRIPT] : <commit_msg>Added missing ')' in the example code.<commit_after>=head1 LICENSE

 Copyright (c) 1999-2013 The European Bioinformatics Institute and
 Genome Research Limited.  All rights reserved.

 This software is distributed under a modified Apache license.
 For license details, please see

   http://www.ensembl.org/info/about/legal/code_licence.html

=head1 CONTACT

 Please email comments or questions to the public Ensembl
 developers list at <<EMAIL>>.

 Questions may also be sent to the Ensembl help desk at
 <<EMAIL>>.

=cut

=head1 NAME

Bio::EnsEMBL::Variation::TranscriptVariation

=head1 SYNOPSIS

    use Bio::EnsEMBL::Variation::TranscriptVariation;

    my $tv = Bio::EnsEMBL::Variation::TranscriptVariation->new(
        -transcript        => $transcript,
        -variation_feature => $var_feat
    );

    print "consequence type: ", (join ",", @{$tv->consequence_type}), "\n";
    print "cdna coords: ", $tv->cdna_start, '-', $tv->cdna_end, "\n";
    print "cds coords: ", $tv->cds_start, '-', $tv->cds_end, "\n";
    print "pep coords: ", $tv->translation_start, '-',$tv->translation_end, "\n";
    print "amino acid change: ", $tv->pep_allele_string, "\n";
    print "codon change: ", $tv->codons, "\n";
    print "allele sequences: ", (join ",", map { $_->variation_feature_seq } 
        @{ $tv->get_all_TranscriptVariationAlleles }), "\n";

=head1 DESCRIPTION

A TranscriptVariation object represents a variation feature which is in close
proximity to an Ensembl transcript. A TranscriptVariation object has several
attributes which define the relationship of the variation to the transcript.

=cut

package Bio::EnsEMBL::Variation::TranscriptVariation;

use strict;
use warnings;

use Bio::EnsEMBL::Utils::Scalar qw(assert_ref check_ref);
use Bio::EnsEMBL::Variation::TranscriptVariationAllele;
use Bio::EnsEMBL::Variation::Utils::VariationEffect qw(overlap within_cds);
use Bio::EnsEMBL::Variation::BaseTranscriptVariation;

use base qw(Bio::EnsEMBL::Variation::BaseTranscriptVariation Bio::EnsEMBL::Variation::VariationFeatureOverlap);

=head2 new

  Arg [-TRANSCRIPT] : 
{'fraction_non_alphanumeric': 0.12987951807228915, 'fraction_numerical': 0.006746987951807229, 'mean_word_length': 4.913105413105413, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 39, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, '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': '4622014', 'n_tokens_mistral': 1397, 'n_tokens_neox': 1309, 'n_words': 359}