Extended alignment tree to include Densoviruses

buildGenusLevelPaleoProjects.glue

@@ -22,5 +22,3 @@ project parvoviridae
 
   exit
 
-
-

buildCompleteProject.glue → buildGenusLevelProjects.glue

@@ -1,25 +1,3 @@
-delete project parvoviridae
-create project parvoviridae "A GLUE project for the Parvoviridae" --minVersion 0.1.66
-
-# Create the database schema
-schema-project parvoviridae
-  run file glue/build/core/parvoSchemaExtensions.glue
-  run file glue/build/core/parvoSchemaExtensionsPaleovirus.glue
-  exit
-
-
-# Load project settings
-project parvoviridae
-  run file glue/build/core/parvoProjectSettings.glue
-  exit
-
-
-# Build the core project for family Parvoviridae (Genus master references only)
-project parvoviridae
-  run file glue/build/core/buildParvoCoreProject.glue
-  exit
-
-
 
 # Build genus-level extensions (Each includes representatives of all species within the genus)
 project parvoviridae
@@ -29,7 +7,7 @@ project parvoviridae
   #run file glue/build/genus/boca/buildBocaProject.glue
 
   #run file glue/build/genus/amdo/buildAmdoProject.glue
-  run file glue/build/genus/proto/buildProtoProject.glue
+  #run file glue/build/genus/proto/buildProtoProject.glue
 
   #run file glue/build/genus/erythro/buildErythroProject.glue
   #run file glue/build/genus/dependo/buildDependoProject.glue
@@ -43,8 +21,3 @@ project parvoviridae
   #run script glue/build/core/refseqsInheritFeatureLocations.js
 
   exit
-
-# Build genus-level paleovirus components of project
-#run file buildGenusLevelPaleoProjects.glue
-
-

glue/build/core/parvoAlignmentTree.glue

@@ -11,21 +11,62 @@
 	extract child AL_Parvovirinae      --refName REF_MASTER_Proto_CPV        # NC_001539
 	demote member AL_Parvovirinae      --whereClause "sequence.subfamily = 'Parvovirinae'"
 
-    extract child AL_Densovirinae      --refName REF_MASTER_Ambidenso_JcDNV  # NC_004284
+    extract child AL_Densovirinae      --refName REF_MASTER_Pefuambidenso_PfDNV  # NC_004284
 	demote member AL_Densovirinae      --whereClause "sequence.subfamily = 'Densovirinae'"
 
     extract child AL_Hamaparvovirinae  --refName REF_MASTER_Chaphama_PPV7 # NC_040562
 	demote member AL_Hamaparvovirinae  --whereClause "sequence.subfamily = 'Hamaparvovirinae'" 	
     exit
 
+
+  # The hamaparvoviruses (Note some genera are still named 'denso-' for legacy reasons)
   alignment AL_Hamaparvovirinae
 
 	extract child AL_CROSS_GENUS_Chaphama_Ichthama --r REF_MASTER_Chaphama_PPV7
 	demote member AL_CROSS_GENUS_Chaphama_Ichthama --whereClause "sequence.genus = 'Chaphamaparvovirus'"
 	demote member AL_CROSS_GENUS_Chaphama_Ichthama --whereClause "sequence.genus = 'Ichthamaparvovirus'"
+
+	extract child AL_GENUS_Penstyldenso --r REF_MASTER_Penstyldenso_IHHN
+	demote member AL_GENUS_Penstyldenso --whereClause "sequence.genus = 'Penstyldensoparvovirus'"
+
+	extract child AL_GENUS_Brevidenso --r REF_MASTER_Brevidenso_AalDNV2
+	demote member AL_GENUS_Brevidenso --whereClause "sequence.genus = 'Brevidensoparvovirus'"
+
+	extract child AL_GENUS_Hepandenso --r REF_MASTER_Hepandenso_FCDNV
+	demote member AL_GENUS_Hepandenso --whereClause "sequence.genus = 'Hepandensoparvovirus'"
     exit
 
 
+  # The densoviruses 
+  alignment AL_Densovirinae
+
+	extract child AL_GENUS_Pefuambidenso --r REF_MASTER_Pefuambidenso_PfDNV
+	demote member AL_GENUS_Pefuambidenso --whereClause "sequence.genus = 'Pefuambidensovirus'"
+
+	extract child AL_GENUS_Ambidenso --r REF_MASTER_Ambidenso_JcDNV
+	demote member AL_GENUS_Ambidenso --whereClause "sequence.genus = 'Ambidensoparvovirus'"
+
+	extract child AL_GENUS_Protoambidenso --r REF_MASTER_Protoambidenso_GmDV
+	demote member AL_GENUS_Protoambidenso --whereClause "sequence.genus = 'Protoambidensovirus'"
+
+	extract child AL_GENUS_Iteradenso --r REF_MASTER_Iteradenso_BmDNV5
+	demote member AL_GENUS_Iteradenso --whereClause "sequence.genus = 'Iteradensoparvovirus'"
+
+	extract child AL_GENUS_Scindoambidenso --r REF_MASTER_Scindoambidenso_PcDV
+	demote member AL_GENUS_Scindoambidenso --whereClause "sequence.genus = 'Scindoambidensovirus'"
+
+ 	extract child AL_GENUS_Blattambidenso --r REF_MASTER_Blattambidenso_BgDV
+	demote member AL_GENUS_Blattambidenso --whereClause "sequence.genus = 'Blattambidensovirus'"
+
+ 	extract child AL_GENUS_Miniambidenso --r REF_MASTER_Miniambidenso_AdMADV
+	demote member AL_GENUS_Miniambidenso --whereClause "sequence.genus = 'Miniambidensovirus'"
+
+ 	extract child AL_GENUS_Aquiambidenso --r REF_MASTER_Aquiambidenso_AaDV
+	demote member AL_GENUS_Aquiambidenso --whereClause "sequence.genus = 'Aquiambidensovirus'" 
+    exit
+
+
+
   #~# Cross-genus
   alignment AL_Parvovirinae
 

glue/build/core/parvoExplicitRefseqFeatureLocations.glue

@@ -553,7 +553,7 @@
 
 
 
-  # Ambidenso
+  # Pefuambidenso
   reference REF_MASTER_Ambidenso_JcDNV
 
  	add feature-location whole_genome

glue/build/core/parvoMasterReferences.glue

@@ -15,16 +15,19 @@
 
 
   ## Densovirinae    
-  create reference REF_MASTER_Ambidenso_JcDNV     ncbi-refseqs NC_004284
-  create reference REF_MASTER_Ambidenso_PfDNV     ncbi-refseqs NC_000936
-  create reference REF_MASTER_Iteradenso_BmDNV-5  ncbi-refseqs NC_004287
-  create reference REF_MASTER_Hepandenso_FCDNV    ncbi-refseqs NC_014357
+  create reference REF_MASTER_Ambidenso_JcDNV        ncbi-refseqs NC_004284
+  create reference REF_MASTER_Pefuambidenso_PfDNV    ncbi-refseqs NC_000936 
+  create reference REF_MASTER_Iteradenso_BmDNV5      ncbi-refseqs NC_004287
+  create reference REF_MASTER_Protoambidenso_GmDV    ncbi-refseqs NC_004286
+  create reference REF_MASTER_Scindoambidenso_PcDV   ncbi-refseqs NC_004289
+  create reference REF_MASTER_Blattambidenso_BgDV    ncbi-refseqs NC_005041
+  create reference REF_MASTER_Miniambidenso_AdMADV   ncbi-refseqs NC_022564
+  create reference REF_MASTER_Aquiambidenso_AaDV     ncbi-refseqs NC_038532
 
 
   ## Hamaparvovirinae    
-  create reference REF_MASTER_Brevidenso_AalDNV-2 ncbi-refseqs NC_004285
+  create reference REF_MASTER_Brevidenso_AalDNV2  ncbi-refseqs NC_004285
   create reference REF_MASTER_Penstyldenso_IHHN   ncbi-refseqs NC_002190
   create reference REF_MASTER_Chaphama_PPV7       ncbi-refseqs NC_040562
   create reference REF_MASTER_Ichthama_SynChPV    ncbi-refseqs MN049932
-
-
+  create reference REF_MASTER_Hepandenso_FCDNV    ncbi-refseqs NC_014357