.. _`bio/busco`:

BUSCO
=====


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/busco?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/busco

Assess assembly and annotation completeness with BUSCO 


**URL**: https://busco.ezlab.org/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule run_busco:
        input:
            "protein.fasta",
        output:
            short_json="txome_busco/short_summary.json",
            short_txt="txome_busco/short_summary.txt",
            full_table="txome_busco/full_table.tsv",
            miss_list="txome_busco/busco_missing.tsv",
            dataset_dir=directory("resources/busco_downloads"),
        log:
            "logs/proteins_busco.log",
        params:
            mode="proteins",
            lineage="stramenopiles_odb10",
            # optional parameters
            extra="",
        threads: 8
        wrapper:
            "v3.0.1/bio/busco"


    rule run_busco_euk:
        input:
            "protein.fasta",
        output:
            out_dir=directory("txome_busco/euk"),
            dataset_dir=directory("resources/busco_downloads"),
        log:
            "logs/proteins_busco_euk.log",
        params:
            mode="proteins",
            # optional parameters
            extra="--auto-lineage-euk",
        threads: 8
        wrapper:
            "v3.0.1/bio/busco"


    rule run_busco_prok:
        input:
            "protein.fasta",
        output:
            out_dir=directory("txome_busco/prok"),
            dataset_dir=directory("resources/busco_downloads"),
        log:
            "logs/proteins_busco_prok.log",
        params:
            mode="proteins",
            # optional parameters
            extra="--auto-lineage-prok",
        threads: 8
        wrapper:
            "v3.0.1/bio/busco"

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.


Notes
-----

* The `lineage` parameter sets the lineage dataset ot use (optional). In `auto-lineage` mode, `output` or `dataset` folders need to be retrieved as a whole, since it is not possible to infer the output file names (they depend on the best lineage match).


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

* ``busco=5.5.0``

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

* Path to assembly fasta

**Output:**

* ``out_dir``: Path to annotation quality files
* ``dataset_dir``: Optional path to dataset directory
* ``short_txt``: Optional path to plain text results summary. Requires parameter `lineage`.
* ``short_json``: Optional path to json formatted results summary. Requires parameter `lineage`.
* ``full_table``: Optional path to TSV formatted results. Requires parameter `lineage`.
* ``miss_list``: Contains a list of missing BUSCOs. Requires parameter `lineage`.



Params
------

* ``lineage``: Assembly lineage.

* ``mode``: Either `genome`, `transcriptome`, and `proteins`

* ``extra``: Optional parameters besides `mode` `--lineage`, `--cpu` and IO files.




Authors
-------

* Tessa Pierce
* Filipe G. Vieira


Code
----

.. code-block:: python

    """Snakemake wrapper for BUSCO assessment"""

    __author__ = "Tessa Pierce"
    __copyright__ = "Copyright 2018, Tessa Pierce"
    __email__ = "ntpierce@gmail.com"
    __license__ = "MIT"


    import tempfile
    from snakemake.shell import shell


    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
    extra = snakemake.params.get("extra", "")


    mode = snakemake.params.get("mode")
    assert mode in [
        "genome",
        "transcriptome",
        "proteins",
    ], "invalid run mode: only 'genome', 'transcriptome' or 'proteins' allowed"


    lineage = lineage_opt = snakemake.params.get("lineage", "")
    if lineage_opt:
        lineage_opt = f"--lineage {lineage_opt}"


    with tempfile.TemporaryDirectory() as tmpdir:
        dataset_dir = snakemake.input.get("dataset_dir", "")
        if not dataset_dir:
            dataset_dir = f"{tmpdir}/dataset"

        shell(
            "busco"
            " --cpu {snakemake.threads}"
            " --in {snakemake.input}"
            " --mode {mode}"
            " {lineage_opt}"
            " {extra}"
            " --download_path {dataset_dir}"
            " --out_path {tmpdir}"
            " --out output"
            " {log}"
        )

        if snakemake.output.get("short_txt"):
            assert lineage, "parameter 'lineage' is required to output 'short_tsv'"
            shell(
                "cat {tmpdir}/output/short_summary.specific.{lineage}.output.txt > {snakemake.output.short_txt:q}"
            )
        if snakemake.output.get("short_json"):
            assert lineage, "parameter 'lineage' is required to output 'short_json'"
            shell(
                "cat {tmpdir}/output/short_summary.specific.{lineage}.output.json > {snakemake.output.short_json:q}"
            )
        if snakemake.output.get("full_table"):
            assert lineage, "parameter 'lineage' is required to output 'full_table'"
            shell(
                "cat {tmpdir}/output/run_{lineage}/full_table.tsv > {snakemake.output.full_table:q}"
            )
        if snakemake.output.get("miss_list"):
            assert lineage, "parameter 'lineage' is required to output 'miss_list'"
            shell(
                "cat {tmpdir}/output/run_{lineage}/missing_busco_list.tsv > {snakemake.output.miss_list:q}"
            )
        if snakemake.output.get("out_dir"):
            shell("mv {tmpdir}/output {snakemake.output.out_dir:q}")
        if snakemake.output.get("dataset_dir"):
            shell("mv {dataset_dir} {snakemake.output.dataset_dir:q}")


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