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docs: edit pass on docs

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rneher committed Oct 19, 2019
1 parent e5c81ae commit fe1caae743ff0a509c577ad033529587f53bdbc7
Showing with 26 additions and 24 deletions.
  1. +1 −1 docs/clades.md
  2. +13 −17 docs/cli.rst
  3. +9 −3 docs/installation.md
  4. +1 −1 docs/parse_meta.md
  5. +2 −2 docs/tb_tutorial.md
@@ -1,4 +1,4 @@
# Labeling clades
# Labeling `clades`

Clades in phylogenetic trees are often named to facilitate discussion of genetic diversity, see for example [seasonal influenza on nextstrain](https://nextstrain.org/flu).
Augur has a command to determine the position of such clade labels and assign sequences to clades.
@@ -10,8 +10,8 @@ Each command is documented below.
You can also run each command with the ``--help`` option, for example ``augur tree --help``, for more information at the command-line.


As an example, we'll look that the ``filter`` command in greater detail using the zika tutorial as template.
This command allows you to selected various subsets of your input data for different types of analysis.
As an example, we'll look that the ``filter`` command in greater detail using material form the `zika tutorial <zika_tutorial.html>`__.
The filter command allows you to selected various subsets of your input data for different types of analysis.
A simple example use of this command would be

.. code-block:: bash
@@ -20,13 +20,15 @@ A simple example use of this command would be
This command will select all sequences with collection date in 2012 or later.
The filter command has a large number of options that allow flexible filtering for many common situations.
One such use-case is the exclusion of sequences that are known to be outliers (e.g.~because of sequencing errors, cell-culture adaptation, ...).
One such use-case is the exclusion of sequences that are known to be outliers (e.g. because of sequencing errors, cell-culture adaptation, ...).
These can be specified in a separate file:
```
BRA/2016/FC_DQ75D1
COL/FLR_00034/2015
...
```

.. code-block:: bash
BRA/2016/FC_DQ75D1
COL/FLR_00034/2015
...
To drop such strains, you can pass the name of this file to the augur filter command:

.. code-block:: bash
@@ -38,15 +40,9 @@ To drop such strains, you can pass the name of this file to the augur filter com
--output filtered.fasta
(To improve legibility, we have wrapped the command across multiple lines.)
If you run this command (you should be able to copy-paste this into your terminal), you should see that one of the sequences in the data set was dropped since its name was in the ``dropped_strain.txt`` file.

.. code:: text

BRA/2016/FC_DQ75D1
COL/FLR_00034/2015
...
If you run this command (you should be able to copy-paste this into your terminal) on the data provided in the `zika tutorial <zika_tutorial.html>`__, you should see that one of the sequences in the data set was dropped since its name was in the ``dropped_strains.txt`` file.

Another common filtering operation is subsetting of data to a achieve a more even spatio-temporal distribution or cut-down data set size to more manageable numbers.
Another common filtering operation is subsetting of data to a achieve a more even spatio-temporal distribution or to cut-down data set size to more manageable numbers.
The filter command allows you to select a specific number of sequences from specific groups, for example one sequence per month from each country:

.. code-block:: bash
@@ -60,4 +56,4 @@ The filter command allows you to select a specific number of sequences from spec
--sequences-per-group 1 \
--output filtered.fasta
This subsampling and filtering will reduce the number of sequences in this tutorial data set from 34 to 24.
This subsampling and filtering will reduce the number of sequences in the tutorial data set from 34 to 24.
@@ -1,13 +1,19 @@
# Installation

## Using pip from PyPi

Augur is written in Python 3 and requires at least Python 3.4.
It's published on [PyPi](https://pypi.org) as [nextstrain-augur](https://pypi.org/project/nextstrain-augur), so you can install it with `pip` like so:

python -m pip install nextstrain-augur
```bash
pip install nextstrain-augur
```

You can also install from a git clone or other copy of the source code by running:

python -m pip install .
```bash
pip install .
```

If your system has both Python 2 and Python 3 installed side-by-side, you may need to use `python3` instead of just `python` (which often defaults to Python 2 when both Python versions are installed).

@@ -32,7 +38,7 @@ On Debian/Ubuntu, you can install them via:

Other Linux distributions will likely have the same packages available, although the names may differ slightly.

## With Conda
## Using Conda

Alternatively, augur itself and all of its dependencies can be installed into a [Conda](https://conda.io/miniconda.html) environment:

@@ -1,4 +1,4 @@
# Parsing metadata from fasta-headers
# `parse` metadata from fasta-headers

If you download sequence data from data bases like GISAID or fludb, there often is an option to include meta data such as dates into the header of fasta files.
This might for example look like this:
@@ -515,7 +515,7 @@ If you did have drug resistance information that you wanted to display, you woul

First, you would want to add a color-by for the total number of drugs each node is resistant to.
Since we gave the label 'Drug_Resistance' when we ran the rule, this will be the name of the option, and the `key`, but we can make the `menuItem` and `legendTitle` different if we wish:
```json
```
"Drug_Resistance": {
"menuItem": "Drug_Resistance",
"legendTitle": "Drug Resistance",
@@ -527,7 +527,7 @@ If you had given a different label when you ran the rule, you would change this

You would then need an option for each drug where you have resistance information (or each FEATURE where you have information).
For example, to show the mutations present that confer resistance to Streptomycin and Rifampicin:
```json
```
"Streptomycin": {
"menuItem": "Streptomycin",
"legendTitle": "Streptomycin Resistance",

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