.. _`bio/entrez/efetch`:

EFETCH
======


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

Obtain data from NCBI and Genbank using Entrez efetch

**URL**: https://www.ncbi.nlm.nih.gov/books/NBK179288/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule get_fasta:
        output:
            "test.fasta",
        log:
            "logs/get_fasta.log",
        params:
            id="KY785484",
            db="nuccore",
            format="fasta",
            # optional mode
            mode=None,
        wrapper:
            "v3.3.3/bio/entrez/efetch"

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
---------------------

* ``entrez-direct=16.2``




Authors
-------

* Johannes Köster


Code
----

.. code-block:: python

    import subprocess as sp
    import sys

    if snakemake.log:
        sys.stderr = open(snakemake.log[0], "w")

    cmd = ["efetch"]


    def add_param(param, required=False):
        if snakemake.params.get(param):
            cmd.extend(["-" + param, snakemake.params[param]])
        elif required:
            raise ValueError("Missing required parameter: " + param)
        else:
            return []


    add_param("id", required=True)
    for param in ["db", "format", "mode"]:
        add_param(param)

    with open(snakemake.output[0], "w") as out:
        sp.run(cmd, stderr=sp.STDOUT, stdout=out, check=True)


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