dada2 taxonomy assignation now use frogs formated dbs

tools/dada2/dada2.yaml

@@ -81,6 +81,7 @@
             #   label: "Marker type",
             #   prompt: "Choose unite as taxonomy source if your marker type is ITS"
             # },
+            
             {
               name: dada2_taxonomypath,
               type: select,

tools/dada2_assign_taxonomy/dada2_assign_taxonomy.rule.snakefile

@@ -7,7 +7,13 @@ rule <step_name>__dada2_assign_taxonomy:
     params:
         output_dir = config["results_dir"] + "/" + config["<step_name>__dada2_assign_taxonomy_output_dir"],
         step_dir = config["<step_name>__dada2_assign_taxonomy_output_dir"],
-        taxonomypath = config["<step_name>__dada2_assign_taxonomy_taxonomypath"],
+        script = config["<step_name>__dada2_assign_taxonomy_script"]
+        #taxonomypath = config["<step_name>__dada2_assign_taxonomy_taxonomypath"],
+        
+        taxonomypath = config["<step_name>__dada2_assign_taxonomy_reference_fasta"],
+        taxfile = config["<step_name>__dada2_assign_taxonomy_reference_fasta"]+"/train_set.fasta",
+        yamlfile = config["<step_name>__FROGS_assign_taxonomy_reference_fasta"]+"/info.yaml",
+
         #OTUabundance = config["<step_name>__dada2_assign_taxonomy_abundance"],
         richness = config["results_dir"] + "/" + config["<step_name>__dada2_assign_taxonomy_output_dir"] + "/richness_mqc.png",
         family = config["results_dir"] + "/" + config["<step_name>__dada2_assign_taxonomy_output_dir"] + "/top20_family_mqc.png",
@@ -19,4 +25,5 @@ rule <step_name>__dada2_assign_taxonomy:
         config["results_dir"]+'/logs/' + config["<step_name>__dada2_assign_taxonomy_output_dir"] + '/dada2_assign_taxonomy_log.txt'
     script:
         config["<step_name>__dada2_assign_taxonomy_script"]
+        
     
\ No newline at end of file

tools/dada2_assign_taxonomy/dada2_assign_taxonomy.script.R

 suppressMessages(library(dada2,quietly=T));print(paste0("dada2: ",packageVersion("dada2")))
 suppressMessages(library(RcppParallel,quietly=T))
 
+#this is adapted from dada2
+#use comment="" to avoid problem in reading trainedset_db_taxid which contains # in some columns
+MBBmakeTaxonomyFasta_RDP <- function(fin, fdb, fout, compress=TRUE) {
+  # Read in the fasta and pull out the taxonomy entries
+  sr <- ShortRead::readFasta(fin)
+  id <- as.character(gsub("\"", "", id(sr)))
+  tax <- sapply(strsplit(id, "\\t"), `[`, 2)
+  tax <- gsub("^Root;", "", tax)
+  tax <- strsplit(tax, ";")
+  # Get the names of the standard 6 taxonomic levels
+  
+  db <- read.table(file=fdb, sep="*", comment.char="", stringsAsFactors=FALSE)
+  colnames(db) <- c("Index", "Name", "L", "R", "Level")
+  keep <- db$Name[db$Level %in% c("domain", "phylum", "class", "order", "family", "genus")]
+  # Cut down to just the 6 level taxonomy
+  tax <- sapply(tax, function(x) x[x %in% keep])
+  tax <- lapply(tax, paste, collapse = ";")
+  tax <- unlist(tax)
+  # Final formatting
+  tax <- paste0(tax, ";") # Ending semicolon
+  tax <- gsub("[^;]*_incertae_sedis;$", "", tax) # Uncertain lowest-level assignment is better to leave blank
+  tax <- gsub(" ", "_", tax)
+  # Write to disk
+  ShortRead::writeFasta(ShortRead(ShortRead::sread(sr), BStringSet::BStringSet(tax)), fout,
+             width=20000L, compress=compress)
+}
 
 ######################
 # Assign taxonomy
@@ -20,17 +46,26 @@ top20family = snakemake@params[["family"]]
 ordination  = snakemake@params[["ordination"]]
 tryRC = snakemake@params[["tryRC"]]
 
+library(yaml)
+yamlfile = paste0(Taxonomypath, "/info.yaml")
+taxURL = read_yaml(yamlfile)$train_set
+#http://genoweb.toulouse.inra.fr/frogs_databanks/assignation/COI/BOLD_COI-5P/BOLD_COI-5P_022019.tar.gz to BOLD_COI-5P_022019.tar.gz
+frogsfile = paste0(Taxonomypath, basename(taxURL))
+marker = gsub(".tar.gz",  "",  basename(taxURL))
+taxfile = paste0(Taxonomypath, "/train_set_",marker,".fa.gz")
+speciesfile = paste0(Taxonomypath, "/assignment_",marker,".fa.gz")
 
-
-taxfile = paste0(Taxonomypath, "/train_set.fa.gz")
-speciesfile = paste0(Taxonomypath, "/assignment.fa.gz")
 if ( ! file.exists(taxfile))
-{
-    library(yaml)
-    yamlfile = paste0(Taxonomypath, "/info.yaml")
-    taxURL = read_yaml(yamlfile)$train_set
+{  
+    download.file(taxURL, frogsfile, "wget")
+    cmd = paste0("cd ",Taxonomypath," && tar -xzf ",frogsfile," && rm -f ", frogsfile);
+    system(cmd)
+    unzipedDir = gsub(".tar.gz", "",  frogsfile)
+    
+    MBBmakeTaxonomyFasta_RDP(paste0(unzipedDir, "/",marker,".fasta"), paste0(unzipedDir, "/",marker,".tax"), taxfile, compress=TRUE) 
+    unlink(unzipedDir, recursive = TRUE, force = TRUE)
+
     speciesURL = read_yaml(yamlfile)$species_assignment
-    download.file(taxURL, taxfile, "wget")
     if(! is.null(speciesURL))
     { download.file(speciesURL, speciesfile, "wget") }
 }

tools/dada2_assign_taxonomy/dada2_assign_taxonomy.yaml

@@ -40,6 +40,32 @@
               step: 1,
               label: "Number of threads to use",
             },
+            {
+              name: dada2_assign_taxonomy_reference_fasta,
+              type: select,
+              choices: [
+                BOLD_COI-5P: "/FROGS_taxonomy/COI/BOLD_COI-5P",
+                MIDORI: "/FROGS_taxonomy/COI/MIDORI",
+                DAIRYdb: "/FROGS_taxonomy/DAIRYdb",
+                Diat.barcode: "/FROGS_taxonomy/Diat.barcode",
+                EZBioCloud: "/FROGS_taxonomy/EZBioCloud",
+                MaarjAM: "/FROGS_taxonomy/MaarjAM",
+                MiDas: "/FROGS_taxonomy/MiDas",
+                PHYMYCO_DB: "/FROGS_taxonomy/PHYMYCO_DB",
+                PR2: "/FROGS_taxonomy/PR2",
+                rbcL: "/FROGS_taxonomy/rbcL",
+                rpoB: "/FROGS_taxonomy/rpoB",
+                silva_138.1_16S: "/FROGS_taxonomy/SILVA/16S",
+                silva_138.1_18S: "/FROGS_taxonomy/SILVA/18S",
+                silva_138.1_23S: "/FROGS_taxonomy/SILVA/23S",
+                silva_138.1_28S: "/FROGS_taxonomy/SILVA/28S ",
+                silva_138.1_LSU: "/FROGS_taxonomy/SILVA/LSU",
+                silva_138.1_SSU: "/FROGS_taxonomy/SILVA/SSU",
+                Unite: "/FROGS_taxonomy/Unite",
+              ],
+              value: "/FROGS_taxonomy/SILVA/16S",
+              label: "Taxonomy source"
+            },
             {
               name: dada2_assign_taxonomy_taxonomypath,
               type: select,
@@ -110,7 +136,8 @@
   },
   data: [
     {
-      name: taxonomy,
+      #name: taxonomy,
+      name: FROGS_taxonomy,
       type: directory
     }
   ],