azulejo 0.7.5

tile phylogenetic space with subtrees

azulejo noun INFORMAL a glazed tile, usually blue, found on the inside of churches and palaces in Spain and Portugal.

azulejo

azulejo azulejo tiles phylogenetic space with subtrees normalizes and validates genomic data files prior to further processing or inclusion in a data store such as that of the Legume Federation.

Prerequisites

Python 3.6 or greater is required. This package is tested under Linux and MacOS using Python 3.7.

Installation for Users

Install via pip or (better yet) pipx:

pipx install azulejo

azulejo contains some long commands and many options. To enable command-line completion for azulejo commands, execute the following command if you are using bash as your shell:

eval "$(_AZULEJO_COMPLETE=source_bash azulejo)"

For Developers

If you plan to develop azulejo, you’ll need to install the poetry dependency manager. If you haven’t previously installed poetry, execute the command:

curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python

Next, get the master branch from GitHub

git clone https://github.com/legumeinfo/azulejo.git

Change to the azulejo/ directory and install with poetry:

poetry install -v

Run azulejo with poetry:

poetry run azulejo

Usage

Installation puts a single script called azulejo in your path. The usage format is:

azulejo [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS][ARGS]

Global Options

The following options are global in scope and, if used must be placed before COMMAND:

-v, –verbose	Log debugging info to stderr.
-q, –quiet	Suppress logging to stderr.
–no-logfile	Suppress logging to file.
-e, –warnings_as_errors	Treat warnings as fatal (for testing).

Commands

A listing of commands is available via azulejo --help. The currently implemented commands are:

add-singletons	Add singleton clusters to cluster file.
adjacency-to-graph	Turn adjacency data into GML graph file.
analyze-clusters	Statistics of clustering as function of identity.
annotate-homology	Marshal homology and sequence information.
cluster-in-steps	Cluster in steps from low to 100% identity.
clusters-to-histograms	Compute histograms from cluster file.
combine-clusters	Combine synteny and homology clusters,
compare-clusters	compare one cluster file with another
dagchainer-synteny	Read DAGchainer synteny into homology frames.
length-std-dist	Plot length distribution of singletons in clusters
outlier-length-dist	Plot length distribution of outliers in clusters.
prepare-protein-files	Sanitize and combine protein FASTA files.
proxy-genes	Calculate a set of proxy genes from synteny files.
synteny-anchors	Calculate synteny anchors.
usearch-cluster	Cluster at a global sequence identity threshold.

Each command has its COMMANDOPTIONS, which may be listed with:

azulejo COMMAND --help

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