.. _`bio/seqkit`:

SEQKIT GENERIC WRAPPER
======================


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

Run SeqKit.


**URL**: https://bioinf.shenwei.me/seqkit/usage/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule seqkit_seq:
        input:
            fasta="data/{sample}.fa",
        output:
            fasta="out/seq/{sample}.fa.gz",
        log:
            "logs/seq/{sample}.log",
        params:
            command="seq",
            extra="--min-len 10",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_subseq_bed:
        input:
            fasta="data/{sample}.fa",
            bed="data/{sample}.bed",
        output:
            fasta="out/subseq/bed/{sample}.fa.gz",
        log:
            "logs/subseq/bed/{sample}.log",
        params:
            command="subseq",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_subseq_gtf:
        input:
            fasta="data/{sample}.fa",
            gtf="data/{sample}.gtf",
        output:
            fasta="out/subseq/gtf/{sample}.fa.gz",
        log:
            "logs/subseq/gtf/{sample}.log",
        params:
            command="subseq",
            extra="--feature CDS",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_subseq_region:
        input:
            fasta="data/{sample}.fa",
        output:
            fasta="out/subseq/region/{sample}.fa.gz",
        log:
            "logs/subseq/region/{sample}.log",
        params:
            command="subseq",
            extra="--region 1:12",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_fx2tab:
        input:
            fastx="data/{sample}.fastq",
        output:
            tsv="out/fx2tab/{sample}.tsv",
        log:
            "logs/fx2tab/{sample}.log",
        params:
            command="fx2tab",
            extra="--name",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_grep_name:
        input:
            fastx="data/{sample}.fastq",
            pattern="data/name.txt",
        output:
            fastx="out/grep/name/{sample}.fastq.gz",
        log:
            "logs/grep/name/{sample}.log",
        params:
            command="grep",
            extra="--by-name",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_grep_seq:
        input:
            fastx="data/{sample}.fastq",
            pattern="data/seq.txt",
        output:
            fastx="out/grep/seq/{sample}.fastq.gz",
        log:
            "logs/grep/seq/{sample}.log",
        params:
            command="grep",
            extra="--by-seq",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_rmdup_name:
        input:
            fastx="data/{sample}.fastq",
        output:
            fastx="out/rmdup/name/{sample}.fastq.gz",
            dup_num="out/rmdup/name/{sample}.num.txt",
            dup_seqs="out/rmdup/name/{sample}.seq.txt",
        log:
            "logs/rmdup/name/{sample}.log",
        params:
            command="rmdup",
            extra="--by-name",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_rmdup_seq:
        input:
            fastx="data/{sample}.fastq",
        output:
            fastx="out/rmdup/seq/{sample}.fastq.gz",
            dup_num="out/rmdup/seq/{sample}.num.txt",
            dup_seqs="out/rmdup/seq/{sample}.seq.txt",
        log:
            "logs/rmdup/seq/{sample}.log",
        params:
            command="rmdup",
            extra="--by-seq",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"


    rule seqkit_stats:
        input:
            fastx="data/{sample}.fastq",
        output:
            stats="out/stats/{sample}.tsv",
        log:
            "logs/stats/{sample}.log",
        params:
            command="stats",
            extra="--all --tabular",
        threads: 2
        wrapper:
            "v3.0.1/bio/seqkit"

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
-----

* First `input` and `output` file is considered to be the main one.
* Keys for extra `input` and `output` files need to match `seqkit` arguments without the `-file` suffix (if present).


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

* ``seqkit=2.6.1``

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

* input file(s)

**Output:**

* output file(s)



Params
------

* ``command``: SeqKit command to use.

* ``extra``: Optional parameters.




Authors
-------

* Filipe G. Vieira


Code
----

.. code-block:: python

    __author__ = "Filipe G. Vieira"
    __copyright__ = "Copyright 2023, Filipe G. Vieira"
    __license__ = "MIT"

    from snakemake.shell import shell


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


    extra_input = " ".join(
        [
            f"--{key.replace('_','-')} {value}"
            if key in ["bed", "gtf"]
            else f"--{key.replace('_','-')}-file {value}"
            for key, value in snakemake.input.items()
        ][1:]
    )

    extra_output = " ".join(
        [
            f"--{key.replace('_','-')} {value}"
            if key in ["read1", "read2"]
            else f"--{key.replace('_','-')}-file {value}"
            for key, value in snakemake.output.items()
        ][1:]
    )


    shell(
        "seqkit {snakemake.params.command}"
        " --threads {snakemake.threads}"
        " {extra_input}"
        " {extra_output}"
        " {extra}"
        " --out-file {snakemake.output[0]}"
        " {snakemake.input[0]}"
        " {log}"
    )


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