Metadata-Version: 2.1
Name: get-assemblies
Version: 0.7.1
Summary: NCBI E-utilities wrapper for assembly downloads
Home-page: https://github.com/davised/get_assemblies
Author: Edward Davis
Author-email: ed@cgrb.oregonstate.edu
Maintainer: Edward Davis
Maintainer-email: ed@cgrb.oregonstate.edu
License: Custom
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: Free for non-commercial use
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
Requires-Dist: rich

get_assemblies
==============

.. contents:: **Table of Contents**
    :backlinks: none

Installation
------------

get_assemblies is distributed on `PyPI
<https://pypi.org/project/get-assemblies>`_ as a universal wheel and is
available on Linux/macOS and supports Python 3.7+. This software will work on
Windows using `WSL
<https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.

get_assemblies depends on `NCBI Entrez Direct <https://www.ncbi.nlm.nih.gov/books/NBK179288/>`_
which requires Perl. Perl is installed by default on most \*nix systems. If
edirect is not currently installed, please run ``get_assemblies --dledirect``
to install.

.. code-block:: bash

    $ python3 -m pip install -U get-assemblies

Dependencies
------------

Python modules:

1. python3-wget
2. tqdm

See ``requirements.txt`` for more info.

External programs:

1. `NCBI Entrez Direct <https://www.ncbi.nlm.nih.gov/books/NBK179288/>`_

You can install external programs using the ``get_assemblies --dledirect``
command. These will be installed to ``${HOME}/edirect`` unless otherwise
specified.

Just tell me how to run it
--------------------------

.. code-block:: bash

    $ get_assemblies organism 'Pseudomonas fluorescens'

^ This will find all genomes tagged as 'Pseudomonas fluorescens' in NCBI's
database. By default, this command will only check to see how many genomes
fall into this category.

To download metadata for the genomes:

.. code-block:: bash

    $ get_assemblies organism 'Pseudomonas fluorescens' --function metadata

Check out the ``metadata.tab`` file that is created after running this command.
Generally you will want to select a subset from your search. One way to do this
is to select the lines that include the genomes of interest, and then saving
the assembly accessions to a file. You can either delete the lines that you
don't want, or use ``grep`` to pull out the lines that you want to keep. Then
you can use ``cut -f 11 > accs.txt`` to get the assembly accesions in a file.

.. code-block:: bash

    $ cat accs.txt | get_assemblies assembly_ids - --function genomes -o fna

This will download the nucleotide fasta files for your genomes of interest.

Overview
--------

This tool was written to make accessing genomic data from NCBI easier. The
output files are renamed such that each assembly has a Genus species strain in
the filename to make it easy to find the genomes that you're interested in. You
won't have to spend time renaming the files by hand.

This software is effectively a wrapper for the NCBI edirect tools that makes
getting genome files easier. If you are interested in starting a comparative
genomics project, this is the tool for you.

The software supports four types of input:

1. organism input, either taxonomy rank names (e.g. Genus species, Family) or
   taxids
2. assembly ids, either accessions or uids
3. nuccore ids (e.g. individual contig/chromosome names)
4. json input (e.g. the intermediate files - docsums - produced by this script)

Five file type outputs are supported:

1. Nucleotide genome sequence (fna)
2. Nucleotide coding sequence (ffn)
3. Amino acid coding sequence (faa)
4. General feature format (i.e. tab-delimited features) (gff)
5. GenBank format (gbk)

The program will attempt to find a unique prefix per genome assembly. This
prefix will be in the resulting filename. A metadata file that contains much
of the relevant information per genome will also be included. This file can
be included as a supplementary table for a manuscript in a comparative genomics
project.

If you need to make phylogenetic trees with these data, check out my other
python package, `automlsa2 <https://pypi.org/project/automlsa2/>`_.

More Examples
-------------

.. code-block:: bash

    $ get_assemblies organism 'Mycobacterium'
    2020-10-15 22:49:53,257 - INFO - Found 7522 genomes to download.
    2020-10-15 22:49:53,257 - INFO - Expect 37610MB to 52654MB of data.

.. code-block:: bash

    $ get_assemblies organism --type ID 167539 --function genomes -o gbk
    2020-10-15 23:10:13,822 - INFO - Found 1 genomes to download.
    2020-10-15 23:10:13,822 - INFO - Expect 5MB to 7MB of data pending the chosen file types for download.
    chunk: 1it [00:01,  1.21s/it]
    docsums: 100%|██████████████████████████████| 1/1 [00:00<00:00, 5146.39it/s]
    2020-10-15 23:10:16,262 - INFO - Downloading 1 files.
    100% [##################################################]           1M / 1M]
    2020-10-15 23:10:18,044 - INFO - P_marinus_CCMP1375_SS120.gbk successfully downloaded.
    download: 100%|███████████████████████████████| 1/1 [00:01<00:00,  1.78s/it]
    $ ls
    docsums0.json       metadata.tab
    get_assemblies.log  P_marinus_CCMP1375_SS120.gbk

.. code-block:: bash

    $ echo GCA_000269645.2 | get_assemblies assembly_ids -
    2020-10-15 23:18:04,107 - INFO - Found 1 genomes to download.
    2020-10-15 23:18:04,107 - INFO - Expect 5MB to 7MB of data pending the chosen file types for download.

Bugs
----

Viruses are currently not handled well, if at all. Look elsewhere to download
those.

Contributing
------------

Feel free to submit bug reports or pull requests so we can improve this
software. Undoubtedly there will be some erroneous prefixes generated out
there, and I'd like to fix them.

Author Contact
--------------

`Ed Davis <mailto:ed@cgrb.oregonstate.edu>`_

Acknowledgments
----------------

Special thanks for helping me test the software and get the python code packaged:

* `Alex Weisberg <https://github.com/alexweisberg>`_
* `Shawn O'Neil <https://github.com/oneilsh>`_

Also, thanks to these groups for supporting me through my scientific career:

* `OSU Chang Lab <https://github.com/osuchanglab>`_
* `Center for Genome Research and Biocomputing @ OSU <https://cgrb.oregonstate.edu>`_

License
-------

get_assemblies is distributed under the terms listed in the ``LICENSE`` file.
The software is free for non-commercial use.

Copyrights
----------

Copyright (c) 2020 Oregon State University

All Rights Reserved.


