.. _`bio/dada2/assign-species`:

DADA2_ASSIGN_SPECIES
====================


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`DADA2 <https://benjjneb.github.io/dada2/index.html>`_
Classifying sequences against a reference database using dada2 ``assignSpecies`` function. Optional parameters are documented in the `manual <https://www.bioconductor.org/packages/release/bioc/manuals/dada2/man/dada2.pdf#assignSpecies>`_ and an example of the function can be found in the dedicated `section <https://benjjneb.github.io/dada2/assign.html#species-assignment>`_ of the DADA2 website.



Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule dada2_assign_species:
        input:
            seqs="results/dada2/seqTab.nochim.RDS", # Chimera-free sequence table
            refFasta="resources/species.fasta" # Reference FASTA for Genus-Species taxonomy
        output:
            "results/dada2/genus-species-taxa.RDS" # Genus-Species 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:
        #    allowMultiple=True
        log:
            "logs/dada2/assign-species/assign-species.log"
        threads: 1 # set desired number of threads here
        wrapper:
            "v3.0.1/bio/dada2/assign-species"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``bioconductor-dada2=1.28.0``

Input/Output
------------
**Input:**

* ``seqs``: RDS file with the chimera-free sequence table
* ``refFasta``: A string with the path to the genus-species FASTA reference database

**Output:**

* RDS file containing the genus and species taxonomic assignments



Params
------

* ``optional arguments for ``assignTaxonomy()``, please provide them as python ``key=value`` pairs``: 




Authors
-------

* Charlie Pauvert


Code
----

.. code-block:: R

    # __author__ = "Charlie Pauvert"
    # __copyright__ = "Copyright 2020, Charlie Pauvert"
    # __email__ = "cpauvert@protonmail.com"
    # __license__ = "MIT"

    # Snakemake wrapper for exact matching of sequences against 
    # a genus-species reference database using dada2 assignSpecies 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"]]
               )
    # 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::assignSpecies()")
    }

    # Perform Genus-Species taxonomic assignments
    taxa<-do.call(assignSpecies, 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()


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