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chore: Reformat README.md to fix markdownlint errors
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Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
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Expand Up @@ -16,30 +16,37 @@ So this is a set of scripts that focuses on the actual genome downloading.

## Installation

```
```bash
pip install ncbi-genome-download
```

Alternatively, clone this repository from GitHub, then run (in a python virtual environment)
```

```bash
pip install .
```

If this fails on older versions of Python, try updating your `pip` tool first:
```

```bash
pip install --upgrade pip
```

and then rerun the `ncbi-genome-download` install.

Alternatively, `ncbi-genome-download` is packaged in `conda`.
Refer the the Anaconda/miniconda site to install a distribution (highly recommended) https://conda.io/miniconda.html
With that installed one can do:
```
Refer the the Anaconda/[miniconda](https://conda.io/miniconda.html) site to
install a distribution (highly recommended). With that installed one can do:

```bash
conda install -c bioconda ncbi-genome-download
```

`ncbi-genome-download` is only developed and tested on Python releases still under active
support by the Python project. At the moment, this means versions 3.7, 3.8, 3.9, 3.10 and 3.11.
Specifically, no attempt at testing under Python versions older than 3.7 is being made.
`ncbi-genome-download` is only developed and tested on Python releases still
under active support by the Python project. At the moment, this means versions
3.7, 3.8, 3.9, 3.10 and 3.11.
Specifically, no attempt at testing under Python versions older than 3.7 is
being made.

If your system is stuck on an older version of Python, consider using a tool like
[Homebrew](http://brew.sh) to obtain a more up-to-date version.
Expand All @@ -49,141 +56,181 @@ If your system is stuck on an older version of Python, consider using a tool lik
## Usage

To download all bacterial RefSeq genomes in GenBank format from NCBI, run the following:
```

```bash
ncbi-genome-download bacteria
```

Downloading multiple groups is also possible:
```

```bash
ncbi-genome-download bacteria,viral
```

**Note**: To see all available groups, see `ncbi-genome-download --help`, or simply use `all` to check all groups.
Naming a more specific group will reduce the download size and the time needed to find the sequences to download.
**Note**: To see all available groups, see `ncbi-genome-download --help`, or
simply use `all` to check all groups. Naming a more specific group will reduce
the download size and the time needed to find the sequences to download.

If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel:
```
If you're on a reasonably fast connection, you might want to try running
multiple downloads in parallel:

```bash
ncbi-genome-download bacteria --parallel 4
```


To download all fungal GenBank genomes from NCBI in GenBank format, run:
```

```bash
ncbi-genome-download --section genbank fungi
```

To download all viral RefSeq genomes in FASTA format, run:
```

```bash
ncbi-genome-download --formats fasta viral
```

It is possible to download multiple formats by supplying a list of formats or simply download all formats:
```
It is possible to download multiple formats by supplying a list of formats or
simply downloading all formats:

```bash
ncbi-genome-download --formats fasta,assembly-report viral
ncbi-genome-download --formats all viral
```

To download only completed bacterial RefSeq genomes in GenBank format, run:
```

```bash
ncbi-genome-download --assembly-levels complete bacteria
```

It is possible to download multiple assembly levels at once by supplying a list:
```

```bash
ncbi-genome-download --assembly-levels complete,chromosome bacteria
```

To download only bacterial reference genomes from RefSeq in GenBank format, run:
```

```bash
ncbi-genome-download --refseq-categories reference bacteria
```

To download bacterial RefSeq genomes of the genus _Streptomyces_, run:
```

```bash
ncbi-genome-download --genera Streptomyces bacteria
```

**Note**: This is a simple string match on the organism name provided by NCBI only.

You can also use this with a slight trick to download genomes of a certain species as well:
```
You can also use this with a slight trick to download genomes of a certain
species as well:

```bash
ncbi-genome-download --genera "Streptomyces coelicolor" bacteria
```

**Note**: The quotes are important. Again, this is a simple string match on the organism
name provided by the NCBI.

Multiple genera is also possible:
```

```bash
ncbi-genome-download --genera "Streptomyces coelicolor,Escherichia coli" bacteria
```

You can also put genus names into a file, one organism per line, e.g.:
```

```bash
Streptomyces
Amycolatopsis
```

Then, pass the path to that file (e.g. `my_genera.txt`) to the `--genera` option, like so:
```
Then, pass the path to that file (e.g. `my_genera.txt`) to the `--genera`
option, like so:

```bash
ncbi-genome-download --genera my_genera.txt bacteria
```
**Note**: The above command will download all _Streptomyces_ and _Amycolatopsis_ genomes from RefSeq.

You can make the string match fuzzy using the `--fuzzy-genus` option. This can be handy if you need to match
a value in the middle of the NCBI organism name, like so:
**Note**: The above command will download all _Streptomyces_ and _Amycolatopsis_
genomes from RefSeq.

```
You can make the string match fuzzy using the `--fuzzy-genus` option. This can
be handy if you need to match a value in the middle of the NCBI organism name,
like so:

```bash
ncbi-genome-download --genera coelicolor --fuzzy-genus bacteria
```
**Note**: The above command will download all bacterial genomes containing "coelicolor" anywhere in their
organism name from RefSeq.

**Note**: The above command will download all bacterial genomes containing
"coelicolor" anywhere in their organism name from RefSeq.

To download bacterial RefSeq genomes based on their NCBI species taxonomy ID, run:
```

```bash
ncbi-genome-download --species-taxids 562 bacteria
```
**Note**: The above command will download all RefSeq genomes belonging to _Escherichia coli_.

**Note**: The above command will download all RefSeq genomes belonging to
_Escherichia coli_.

To download a specific bacterial RefSeq genomes based on its NCBI taxonomy ID, run:
```

```bash
ncbi-genome-download --taxids 511145 bacteria
```
**Note**: The above command will download the RefSeq genome belonging to _Escherichia coli str. K-12 substr. MG1655_.

It is also possible to download multiple species taxids or taxids by supplying the numbers in a comma-separated list:
```
**Note**: The above command will download the RefSeq genome belonging to
_Escherichia coli str. K-12 substr. MG1655_.

It is also possible to download multiple species taxids or taxids by supplying
the numbers in a comma-separated list:

```bash
ncbi-genome-download --taxids 9606,9685 --assembly-level chromosome vertebrate_mammalian
```

**Note**: The above command will download the reference genomes for cat and human.

In addition, you can put multiple species taxids or taxids into a file, one per line
and pass that filename to the `--species-taxids` or `--taxids` parameters, respectively.

Assuming you had a file `my_taxids.txt` with the following contents:
```

```text
9606
9685
```

You could download the reference genomes for cat and human like this:
```

```bash
ncbi-genome-download --taxids my_taxids.txt --assembly-levels chromosome vertebrate_mammalian
```

It is possible to also create a human-readable directory structure in parallel to mirroring
the layout used by NCBI:
```
It is possible to also create a human-readable directory structure in parallel
to mirroring the layout used by NCBI:

```bash
ncbi-genome-download --human-readable bacteria
```

This will use links to point to the appropriate files in the NCBI directory structure,
so it saves file space. Note that links are not supported on some Windows file systems and some
older versions of Windows.
so it saves file space. Note that links are not supported on some Windows file
systems and some older versions of Windows.

It is also possible to re-run a previous download with the `--human-readable` option.
In this case, `ncbi-genome-download` will not download any new genome files, and just create
human-readable directory structure. Note that if any files have been changed on the NCBI side,
a file download will be triggered.
In this case, `ncbi-genome-download` will not download any new genome files, and
just create human-readable directory structure. Note that if any files have been
changed on the NCBI side, a file download will be triggered.

There is a "dry-run" option to show which accessions would be downloaded, given your filters:
```
There is a "dry-run" option to show which accessions would be downloaded, given
your filters:

```bash
ncbi-genome-download --dry-run bacteria
```

Expand All @@ -193,42 +240,48 @@ values are "any", "all", "type", "reference", "synonym", "proxytype", and/or
"neotype". "any" will include assemblies with no relation to type material
value defined, "all" will download only assemblies with a defined value.
Multiple values can be given, separated by comma:
```

```bash
ncbi-genome-download --type-materials type,reference
```

By default, ncbi-genome-download caches the assembly summary files for the respective taxonomic
groups for one day. You can skip using the cache file by using the `--no-cache` option.
The output of `--help` also shows the cache directory, should you want to remove any of the cached
files.
By default, ncbi-genome-download caches the assembly summary files for the
respective taxonomic groups for one day. You can skip using the cache file by
using the `--no-cache` option. The output of `--help` also shows the cache
directory, should you want to remove any of the cached files.

To get an overview of all options, run
```

```bash
ncbi-genome-download --help
```

### As a method
You can also use it as a method call. Pass the pythonised keyword arguments (`_` instead of `-`)
as described above or in the `--help`:
```

You can also use it as a method call. Pass the pythonised keyword arguments
(`_` instead of `-`) as described above or in the `--help`:

```python
import ncbi_genome_download as ngd
ngd.download()
```
**Note**: To specify a taxonomic group, like *bacteria*, use the `group` keyword.

**Note**: To specify a taxonomic group, like _bacteria_, use the `group` keyword.

### Contributed Scripts: `gimme_taxa.py`
This script lets you find out what TaxIDs to pass to `ngd`, and will write a simple one-item-per-line
file to pass in to it. It utilises the `ete3` toolkit, so refer to their site to install the dependency
if it's not already satisfied.

You can query the database using a particular TaxID, or a scientific name. The primary function of the
script is to return all the child taxa of the specified parent taxa. The script has various options
for what information is written in the output.
This script lets you find out what TaxIDs to pass to `ngd`, and will write a
simple one-item-per-line file to pass in to it. It utilises the `ete3` toolkit,
so refer to their site to install the dependency if it's not already satisfied.

You can query the database using a particular TaxID, or a scientific name. The
primary function of the script is to return all the child taxa of the specified
parent taxa. The script has various options for what information is written in
the output.

A basic invocation may look like:

```
```bash
# Fetch all descendent taxa for Escherichia (taxid 561):
python gimme_taxa.py -o ~/mytaxafile.txt 561

Expand All @@ -240,18 +293,20 @@ python gimme_taxa.py -o all_descendent_taxids.txt 561,Methanobrevibacter
```

On first use, a small sqlite database will be created in your home directory
by default (change the location with the `--database` flag). You can update this database
by using the `--update` flag. Note that if the database is not in your home directory,
you must specify it with `--database` or a new database will be created in your home
directory.
by default (change the location with the `--database` flag). You can update this
database by using the `--update` flag. Note that if the database is not in your
home directory, you must specify it with `--database` or a new database will be
created in your home directory.

To see all help:
```

```bash
python gimme_taxa.py
python gimme_taxa.py -h
python gimme_taxa.py --help
```

## License

All code is available under the Apache License version 2, see the
[`LICENSE`](LICENSE) file for details.

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