Bio::EnsEMBL::Utils::VegaCuration::Gene Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::VegaCuration::Gene:
Public Member Functions | |
| public Int | find_gaps () |
| Public Member Functions inherited from Bio::EnsEMBL::Utils::ConversionSupport | |
| public Bio::EnsEMBL::Utils::ConversionSupport | new () |
| public Boolean | parse_common_options () |
| public Boolean | parse_extra_options () |
| public Array | allowed_params () |
| public Array | get_common_params () |
| public Array | get_loutre_params () |
| public Array | get_annotrack_params () |
| public void | remove_vega_params () |
| public Boolean | confirm_params () |
| public String | list_all_params () |
| public String | create_commandline_options () |
| public Boolean | check_required_params () |
| public Boolean | user_proceed () |
| public String | read_user_input () |
| public Boolean | comma_to_list () |
| public Boolean | list_or_file () |
| public Scalar | param () |
| public String | error () |
| public Int | warnings () |
| public String | serverroot () |
| public DBAdaptor | get_database () |
| public DBI | get_dbconnection () |
| public Bio::EnsEMBL::DBSQL::DBAdaptor | dba () |
| public Boolean | dynamic_use () |
| public Hashref | get_chrlength () |
| public Hashref | get_ensembl_chr_mapping () |
| public Int | get_taxonomy_id () |
| public String | get_species_scientific_name () |
| public String | species () |
| public List | sort_chromosomes () |
| protected Values | _by_chr_num () |
| public Hashref | split_chromosomes_by_size () |
| public Boolean | is_patch () |
| public Boolean | log () |
| public | lock_log () |
| public | unlock_log () |
| public Boolean | log_warning () |
| public void | log_error () |
| public Boolean | log_verbose () |
| public Boolean | log_stamped () |
| public Filehandle | log_filehandle () |
| public Filehandle | filehandle () |
| public Filehandle | init_log_date () |
| public Filehandle | init_log () |
| public Boolean | finish_log () |
| public String | date_and_mem () |
| public String | date () |
| public String | date_and_time () |
| public | date_format () |
| public String | mem () |
| public A | commify () |
| public Arrayref | fetch_non_hidden_slices () |
| public Arrayref | get_non_hidden_slice_names () |
| public Arrayref | get_wanted_chromosomes () |
| public Boolean | is_haplotype () |
| public Arrayref | get_unique_genes () |
| public | get_attrib_values () |
| public Arrayref | fix_attrib_value () |
| protected Attrib_type | _get_attrib_id () |
| public Array_ref | store_new_attribute () |
| public Array_ref | update_attribute () |
| public void | remove_duplicate_attribs () |
| public | save_seq () |
| public String | get_alignment () |
| public | allowed_duplicate_regions () |
Detailed Description
Member Function Documentation
◆ find_gaps()
| public Int Bio::EnsEMBL::Utils::VegaCuration::Gene::find_gaps | ( | ) |
Args : arrayref of B::E::Transcripts Example :
my $gaps = find_gaps($all_transcripts)
Description: identifies regions of a gene that are not covered by any transcript Returntype : int Exceptions : none Caller : internal
Code:
click to view
The documentation for this class was generated from the following file:
- ensembl/modules/Bio/EnsEMBL/Utils/VegaCuration/Gene.pm
