From 14a2116f088fd57c09ee0c2888091c0f70a3228f Mon Sep 17 00:00:00 2001 From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com> Date: Tue, 23 Sep 2025 08:18:01 +0100 Subject: [PATCH 1/2] Project MGI gene names and desc from reference mouse to all strains --- ...GeneNameDescProjection_vertebrates_conf.pm | 63 +++++++++---------- 1 file changed, 30 insertions(+), 33 deletions(-) diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm index 5b5b386df..79d6f24ce 100644 --- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm +++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm @@ -66,22 +66,34 @@ sub default_options { source => 'mus_musculus', taxons => ['Castorimorpha','Myomorpha'], antispecies => [ - 'mus_musculus', - 'mus_musculus_129s1svimj', - 'mus_musculus_aj', - 'mus_musculus_akrj', - 'mus_musculus_balbcj', - 'mus_musculus_c3hhej', - 'mus_musculus_c57bl6nj', - 'mus_musculus_casteij', - 'mus_musculus_cbaj', - 'mus_musculus_dba2j', - 'mus_musculus_fvbnj', - 'mus_musculus_lpj', - 'mus_musculus_nodshiltj', - 'mus_musculus_nzohlltj', - 'mus_musculus_pwkphj', - 'mus_musculus_wsbeij' + 'mus_musculus' + ], + gene_name_source => ['MGI'], + project_trans_names => 1, + }, + { + source => 'mus_musculus', + species => [ + 'mus_musculus_129s1svimj', + 'mus_musculus_aj', + 'mus_musculus_akrj', + 'mus_musculus_balbcj', + 'mus_musculus_c3hhej', + 'mus_musculus_c57bl6nj', + 'mus_musculus_casteij', + 'mus_musculus_cbaj', + 'mus_musculus', + 'mus_musculus_dba2j', + 'mus_musculus_fvbnj', + 'mus_musculus_lpj', + 'mus_musculus_molossinusjf1msj', + 'mus_musculus_nodshiltj', + 'mus_musculus_nzohlltj', + 'mus_musculus_pwkphj', + 'mus_musculus_wsbeij' + ], + antispecies => [ + 'mus_musculus' ], gene_name_source => ['MGI'], project_trans_names => 1, @@ -97,7 +109,7 @@ sub default_options { { source => 'homo_sapiens', taxons => ['Actinopterygii','Cyclostomata','Chondrichthyes'], - antispecies => ['homo_sapiens'], + antispecies => ['homo_sapiens', 'danio_rerio'], gene_name_source => ['HGNC'], project_trans_names => 1, homology_types_allowed => ['ortholog_one2one','ortholog_one2many'], @@ -123,22 +135,7 @@ sub default_options { source => 'mus_musculus', taxons => ['Castorimorpha','Myomorpha'], antispecies => [ - 'mus_musculus', - 'mus_musculus_129s1svimj', - 'mus_musculus_aj', - 'mus_musculus_akrj', - 'mus_musculus_balbcj', - 'mus_musculus_c3hhej', - 'mus_musculus_c57bl6nj', - 'mus_musculus_casteij', - 'mus_musculus_cbaj', - 'mus_musculus_dba2j', - 'mus_musculus_fvbnj', - 'mus_musculus_lpj', - 'mus_musculus_nodshiltj', - 'mus_musculus_nzohlltj', - 'mus_musculus_pwkphj', - 'mus_musculus_wsbeij' + 'mus_musculus' ], gene_name_source => ['MGI'], gene_desc_rules => [], From 7262b2bcad9c4e03d1644af846eaeb6c64f68748 Mon Sep 17 00:00:00 2001 From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com> Date: Tue, 23 Sep 2025 08:35:10 +0100 Subject: [PATCH 2/2] Project MGI Mouse reference gene names and desc to all mouse strains --- ...GeneNameDescProjection_vertebrates_conf.pm | 27 ------------------- 1 file changed, 27 deletions(-) diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm index 79d6f24ce..863dc5f10 100644 --- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm +++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm @@ -71,33 +71,6 @@ sub default_options { gene_name_source => ['MGI'], project_trans_names => 1, }, - { - source => 'mus_musculus', - species => [ - 'mus_musculus_129s1svimj', - 'mus_musculus_aj', - 'mus_musculus_akrj', - 'mus_musculus_balbcj', - 'mus_musculus_c3hhej', - 'mus_musculus_c57bl6nj', - 'mus_musculus_casteij', - 'mus_musculus_cbaj', - 'mus_musculus', - 'mus_musculus_dba2j', - 'mus_musculus_fvbnj', - 'mus_musculus_lpj', - 'mus_musculus_molossinusjf1msj', - 'mus_musculus_nodshiltj', - 'mus_musculus_nzohlltj', - 'mus_musculus_pwkphj', - 'mus_musculus_wsbeij' - ], - antispecies => [ - 'mus_musculus' - ], - gene_name_source => ['MGI'], - project_trans_names => 1, - }, { source => 'danio_rerio', taxons => ['Actinopterygii','Cyclostomata','Coelacanthimorpha','Chondrichthyes'],