/ 
Bio-EnsEMBL-113.0.0
River stage zero No dependents
/ Bio::EnsEMBL::Utils::VegaCuration::Transcript

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

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NAME

SYNOPSIS

DESCRIPTION

METHODS

find_non_overlaps

Args       : arrayref of B::E::Transcripts
Example    : find_non_overlaps($all_transcripts)
Description: identifies any non-overlapping transcripts
Returntype : array refs of stable IDs
Exceptions : none

check_remarks_and_update_names

Arg[1]     : B::E::Gene (with potentially duplicated transcript names)
Arg[2]     : counter 1 (no. of patched genes)
Arg[3]     : counter 2 (no. of patched transcripts)
Example    : $support->update_names($gene,\$c1,\$c2)
Description: - checks remarks and patches transcripts with identical names according to
             CDS and length
Returntype : true | false (depending on whether patched or not), counter1, counter2

check_names_and_overlap

Arg[1]     : arayref of arrayrefs of duplicated names
Arg[2]     : B::E::Gene (with potentially duplicated transcript names)
Arg[3]     : FH (to log new duplicates)
Example    : $support->check_names_and_overlap($transcripts,$gene,$fh)
Description: checks pairs of transcripts identified as having duplicate Vega names:
             - to see if they have identical names in loutre (shouldn't have)
             - distinguish between overlapping and non overlapping transcripts
Returntype : none

get_havana_fragmented_loci_comments

Args       : none
Example    : my $results = $support->get_havana_fragmented_loci_comments
Description: parses the HEREDOC containing Havana comments in this module
Returntype : hashref