DADA2_ASSIGN_TAXONOMY¶
DADA2
Classifying sequences against a reference database using dada2 assignTaxonomy
function. Optional parameters are documented in the manual and the function is introduced in the dedicated tutorial section.
URL:
Example¶
This wrapper can be used in the following way:
rule dada2_assign_taxonomy:
input:
seqs="results/dada2/seqTab.nochim.RDS", # Chimera-free sequence table
refFasta="resources/example_train_set.fa.gz" # Reference FASTA for taxonomy
output:
"results/dada2/taxa.RDS" # Taxonomic assignments
# Even though this is an R wrapper, use named arguments in Python syntax
# here, to specify extra parameters. Python booleans (`arg1=True`, `arg2=False`)
# and lists (`list_arg=[]`) are automatically converted to R.
# For a named list as an extra named argument, use a python dict
# (`named_list={name1=arg1}`).
#params:
# verbose=True
log:
"logs/dada2/assign-taxonomy/assign-taxonomy.log"
threads: 1 # set desired number of threads here
wrapper:
"v1.2.0/bio/dada2/assign-taxonomy"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Software dependencies¶
bioconductor-dada2==1.16
Input/Output¶
Input:
seqs
: RDS file with the chimera-free sequence tablerefFasta
: A string with the path to the FASTA reference database
Output:
- RDS file containing the taxonomic assignments
Params¶
optional arguments for ``assignTaxonomy()
, please provide them as pythonkey=value
pairs``:
Authors¶
- Charlie Pauvert
Code¶
# __author__ = "Charlie Pauvert"
# __copyright__ = "Copyright 2020, Charlie Pauvert"
# __email__ = "cpauvert@protonmail.com"
# __license__ = "MIT"
# Snakemake wrapper for classifying sequences against
# a reference database using dada2 assignTaxonomy function.
# Sink the stderr and stdout to the snakemake log file
# https://stackoverflow.com/a/48173272
log.file<-file(snakemake@log[[1]],open="wt")
sink(log.file)
sink(log.file,type="message")
library(dada2)
# Prepare arguments (no matter the order)
args<-list(
seqs = readRDS(snakemake@input[["seqs"]]),
refFasta = snakemake@input[["refFasta"]],
multithread=snakemake@threads
)
# Check if extra params are passed
if(length(snakemake@params) > 0 ){
# Keeping only the named elements of the list for do.call()
extra<-snakemake@params[ names(snakemake@params) != "" ]
# Add them to the list of arguments
args<-c(args, extra)
} else{
message("No optional parameters. Using default parameters from dada2::assignTaxonomy()")
}
# Learn errors rates for both read types
taxa<-do.call(assignTaxonomy, args)
# Store the taxonomic assignments as a RDS file
saveRDS(taxa, snakemake@output[[1]],compress = T)
# Proper syntax to close the connection for the log file
# but could be optional for Snakemake wrapper
sink(type="message")
sink()