<commit_before>=head1 NAME

Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils - utilities for transcript objects

=head1 SYNOPSIS

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils qw(clone_Transcript);

  or 

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils 

  to get all methods

=head1 DESCRIPTION

All methods in this class should take a Bio::EnsEMBL::Transcript
object as their first argument.

The methods provided should carry out some standard 
functionality for said objects such as printing info, and 
cloning and checking phase consistency or splice sites etc

=head1 CONTACT

please send any questions to <EMAIL>

=head1 METHODS

the rest of the documention details the exported static
class methods

=cut

# $Source: /tmp/ENSCOPY-ENSEMBL-ANALYSIS/modules/Bio/EnsEMBL/Analysis/Tools/GeneBuildUtils/TranscriptUtils.pm,v $
# $Revision: 1.84 $
package Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils;

use strict;
use warnings;
use Exporter;

use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning stack_trace_dump);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranslationUtils qw(print_Translation clone_Translation print_peptide);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonUtils qw(print_Exon clone_Exon Exon_info exon_length_less_than_maximum Exon_info get_upstream_Intron get_downstream_Intron get_upstream_splice_sites get_downstream_splice_sites validate_Exon_coords);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::IntronUtils qw(intron_length_less_than_maximum get_splice_sites);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils qw(seq_region_coord_string id empty_Object);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::EvidenceUtils qw (print_Evidence clone_Evidence);
use Bio::EnsEMBL::Analysis::Tools::Utilities qw(write_seqfile);
use Bio::EnsEMBL::Gene;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::Analysis::Tools::Logger qw(logger_info);

use Bio::EnsEMBL::Analysis;
use Bio::SeqIO;



use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg;


use vars qw (@ISA @EXPORT);

@ISA = qw(Exporter);
@EXPORT = qw(
             all_exons_are_valid
             are_phases_consistent
             are_splice_sites_canonical
             are_strands_consistent
             attach_Slice_to_Transcript
             attach_Analysis_to_Transcript
             attach_Analysis_to_Transcript_no_support
             calculate_exon_phases
             clone_Transcript
             coding_coverage
             convert_to_genes
             convert_translateable_exons_to_exon_extended_objects
             count_non_canonical_splice_sites
             count_real_introns
             dump_cDNA_file
             empty_Transcript
             evidence_coverage
             evidence_coverage_greater_than_minimum
             exon_lengths_all_less_than_maximum
             exonic_proportion
             fully_load_Transcript
             get_downstream_Intron_from_Exon
             get_downstream_splice_sites<commit_msg>Mystery solved.  The Seg module was indirectly pulling in the Runnable base class, which masked an error in TrancriptConsesus (it didn't "use" its base class).  The Seg module is no longer used here.<commit_after>=head1 NAME

Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils - utilities for transcript objects

=head1 SYNOPSIS

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils qw(clone_Transcript);

  or 

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils 

  to get all methods

=head1 DESCRIPTION

All methods in this class should take a Bio::EnsEMBL::Transcript
object as their first argument.

The methods provided should carry out some standard 
functionality for said objects such as printing info, and 
cloning and checking phase consistency or splice sites etc

=head1 CONTACT

please send any questions to <EMAIL>

=head1 METHODS

the rest of the documention details the exported static
class methods

=cut

# $Source: /tmp/ENSCOPY-ENSEMBL-ANALYSIS/modules/Bio/EnsEMBL/Analysis/Tools/GeneBuildUtils/TranscriptUtils.pm,v $
# $Revision: 1.85 $
package Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils;

use strict;
use warnings;
use Exporter;

use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning stack_trace_dump);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranslationUtils qw(print_Translation clone_Translation print_peptide);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::ExonUtils qw(print_Exon clone_Exon Exon_info exon_length_less_than_maximum Exon_info get_upstream_Intron get_downstream_Intron get_upstream_splice_sites get_downstream_splice_sites validate_Exon_coords);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::IntronUtils qw(intron_length_less_than_maximum get_splice_sites);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils qw(seq_region_coord_string id empty_Object);
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::EvidenceUtils qw (print_Evidence clone_Evidence);
use Bio::EnsEMBL::Analysis::Tools::Utilities qw(write_seqfile);
use Bio::EnsEMBL::Gene;
use Bio::EnsEMBL::Transcript;
use Bio::EnsEMBL::Translation;
use Bio::EnsEMBL::Analysis::Tools::Logger qw(logger_info);

use Bio::EnsEMBL::Analysis;
use Bio::SeqIO;

use vars qw (@ISA @EXPORT);

@ISA = qw(Exporter);
@EXPORT = qw(
             all_exons_are_valid
             are_phases_consistent
             are_splice_sites_canonical
             are_strands_consistent
             attach_Slice_to_Transcript
             attach_Analysis_to_Transcript
             attach_Analysis_to_Transcript_no_support
             calculate_exon_phases
             clone_Transcript
             coding_coverage
             convert_to_genes
             convert_translateable_exons_to_exon_extended_objects
             count_non_canonical_splice_sites
             count_real_introns
             dump_cDNA_file
             empty_Transcript
             evidence_coverage
             evidence_coverage_greater_than_minimum
             exon_lengths_all_less_than_maximum
             exonic_proportion
             fully_load_Transcript
             get_downstream_Intron_from_Exon
             get_downstream_splice_sites
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