=pod =head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] 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. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =head1 NAME Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf; =head1 SYNOPSIS init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf To run on a species_set: init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf -species_set_name or init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf -species_set_id To run on a pair of species: init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf -species1 homo_sapiens -species2 gallus_gallus =head1 DESCRIPTION This pipeline uses whole genome alignments to calculate the coverage of homologous pairs. The coverage is calculated on both exonic and intronic regions seperately and summarised using a quality_score calculation The average quality_score between both members of the homology will be written to the homology table (in compara_db option) http://www.ebi.ac.uk/seqdb/confluence/display/EnsCom/Quality+metrics+for+the+orthologs Additional options: -compara_db database containing relevant data (this is where final scores will be written) -alt_aln_dbs take alignment objects from different sources (arrayref of urls or aliases) -alt_homology_db take homology objects from a different source Note: If you wish to use homologies from one database, but the alignments live in a different database, remember that final scores will be written to the homology table of the appointed compara_db. So, if you'd like the final scores written to the homology database, assign this as compara_db and use the alt_aln_dbs option to specify the location of the alignments. Likewise, if you want the scores written to the alignment-containing database, assign it as compara_db and use the alt_homology_db option. Examples: --------- # scores go to homology db, alignments come from afar init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf -compara_db compara_alias -alt_aln_dbs [mysql://ro_user@hosty_mchostface/alignments] # scores go to alignment db init_pipeline.pl Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf -compara_db mysql://user:pass@host/alignments -alt_homology_db homology_alias =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut package Bio::EnsEMBL::Compara::PipeConfig::OrthologQM_Alignment_conf; use strict; use warnings; use Bio::EnsEMBL::Hive::Version 2.4; use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf; # use base ( 'Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf' ); use base ('Bio::EnsEMBL::Compara::PipeConfig::ComparaGeneric_conf'); sub hive_meta_table { my ($self) = @_; return { %{$self->SUPER::hive_meta_table}, # here we inherit anything from the base class 'hive_use_param_stack' => 1, # switch on the new param_stack mechanism }; } sub default_pipeline_name { # Instead of ortholog_qm_alignment my ($self) = @_; return $self->o('member_type') . '_orth_qm_wga'; } sub default_options { my ($self) = @_; return { %{$self->SUPER::default_options}, # inherit the generic ones 'species1' => undef, 'species2' => undef, 'species_set_name' => undef, 'species_set_id' => undef, 'ref_species' => undef, # 'alt_aln_dbs' => undef, 'alt_aln_dbs' => [ ], 'alt_homology_db' => undef, 'orth_batch_size' => 10, # set how many orthologs should be flowed at a time }; } =head2 pipeline_create_commands Description: create tables for writing data to =cut sub pipeline_create_commands { my $self = shift; return [ @{ $self->SUPER::pipeline_create_commands }, $self->db_cmd( 'CREATE TABLE ortholog_quality ( homology_id INT NOT NULL, genome_db_id INT NOT NULL, alignment_mlss INT NOT NULL, combined_exon_coverage FLOAT(5,2) NOT NULL, combined_intron_coverage FLOAT(5,2) NOT NULL, quality_score FLOAT(5,2) NOT NULL, exon_length INT NOT NULL, intron_length INT NOT NULL, INDEX (homology_id) )'), ]; } sub pipeline_wide_parameters { my ($self) = @_; return { %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base class 'ensembl_release' => $self->o('ensembl_release'), 'orth_batch_size' => 10, }; } sub pipeline_analyses { my ($self) = @_; return [ { -logic_name => 'pair_species', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::PairCollection', -flow_into => { '2->B' => [ 'select_mlss' ], 'B->1' => [ 'copy_compara_tables' ], '3' => [ 'reset_mlss' ], }, -input_ids => [{ 'species_set_name' => $self->o('species_set_name'), 'species_set_id' => $self->o('species_set_id'), 'ref_species' => $self->o('ref_species'), 'species1' => $self->o('species1'), 'species2' => $self->o('species2'), 'compara_db' => $self->o('compara_db'), 'alt_aln_dbs' => $self->o('alt_aln_dbs'), 'master_db' => $self->o('master_db'), 'alt_homology_db' => $self->o('alt_homology_db'), 'previous_rel_db' => $self->o('previous_rel_db'), 'member_type' => $self->o('member_type'), }], }, { -logic_name => 'reset_mlss', -module => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd', -parameters => { 'sql' => 'DELETE FROM ortholog_quality WHERE alignment_mlss = #aln_mlss_id#', }, -analysis_capacity => 3, }, { -logic_name => 'select_mlss', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::SelectMLSS', -flow_into => { 1 => [ '?accu_name=alignment_mlsses&accu_address=[]&accu_input_variable=accu_dataflow' ], 2 => [ '?accu_name=mlss_db_mapping&accu_address={mlss_id}&accu_input_variable=mlss_db' ], }, -rc_name => '500Mb_job', -analysis_capacity => 50, }, { -logic_name => 'copy_compara_tables', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::PrepTableCopy', -parameters => { 'copy_chunk_size' => 10, 'program' => $self->o('populate_new_database_exe'), 'reg_conf' => $self->o('reg_conf'), 'master_db' => $self->o('master_db'), 'pipeline_db' => $self->pipeline_url(), }, -flow_into => { '3->C' => [ 'copy_genomic_align_blocks', 'copy_mlss_tags' ], 'C->2' => [ 'copy_funnel' ] }, -analysis_capacity => 1, -rc_name => '1Gb_job' }, { -logic_name => 'copy_genomic_align_blocks', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'where' => 'method_link_species_set_id IN ( #expr( join( ",", @{ #mlss_id_list# } ) )expr# )', 'table' => 'genomic_align_block', 'mode' => 'topup', }, -analysis_capacity => 1, -flow_into => { 1 => [ 'copy_genomic_aligns' ] }, }, { -logic_name => 'copy_genomic_aligns', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'where' => 'method_link_species_set_id IN ( #expr( join( ",", @{ #mlss_id_list# } ) )expr# )', 'table' => 'genomic_align', 'mode' => 'topup', }, -analysis_capacity => 1, }, { -logic_name => 'copy_mlss_tags', -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer', -parameters => { 'where' => 'method_link_species_set_id IN ( #expr( join( ",", @{ #mlss_id_list# } ) )expr# )', 'table' => 'method_link_species_set_tag', 'mode' => 'topup', }, -analysis_capacity => 1, }, { -logic_name => 'copy_funnel', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::CopyFunnel', -flow_into => { 2 => [ 'prepare_orthologs' ], } }, { -logic_name => 'prepare_orthologs', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::PrepareOrthologs', -analysis_capacity => 50, # use per-analysis limiter -flow_into => { 2 => [ 'calculate_wga_coverage' ], 3 => [ 'reuse_wga_score' ], }, -rc_name => '2Gb_job', }, { -logic_name => 'calculate_wga_coverage', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::CalculateWGACoverage', -hive_capacity => 30, -batch_size => 10, -parameters => { pipeline_url => $self->pipeline_url }, -flow_into => { '1' => [ '?table_name=ortholog_quality' ], '2' => [ 'assign_wga_coverage_score' ], }, -rc_name => '2Gb_job', }, { -logic_name => 'assign_wga_coverage_score', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::AssignQualityScore', -hive_capacity => 100, -batch_size => 10, }, { -logic_name => 'reuse_wga_score', -module => 'Bio::EnsEMBL::Compara::RunnableDB::OrthologQM::ReuseWGAScore', -hive_capacity => 30, -batch_size => 10, }, ]; } 1;