azulejo noun INFORMAL a glazed tile, usually blue, found on the inside of churches and palaces in Spain and Portugal.
azulejo
azulejo combines homology and synteny information to
tile phylogenetic space.
The inputs to azulejo
are FASTA files of nucleotide-space
sequences of primary-transcript protein genes and their associated GFF files.
Outputs are sets of proxy gene fragments chosen for
their concordance in multiple sequence alignments, along with
subtrees.
Python 3.7 or greater is required. azulejo
is tested under Linux
using Python 3.8 and 3.9 and under MacOS Big Sur using XCode command-line tools
system Python (currently 3.8). Mac users should see the instructions
on configuring their systems. Installation on BSD is not
supported because many of the python dependencies lack BSD wheels.
We recommend you install azulejo
into its own virtual environment due
to the large number of python dependencies. The easiest way for most
users to install and maintain up-to-date virtual environments is via the
tool pipx. If your system does
not have pipx
installed, you can do so via the commands:
python3 -m pip install --user --upgrade pip python3 -m pip install --user --upgrade pipx python3 -m pipx ensurepath
Follow any instructions that the last command produces about starting a new shell if necessary.
If you choose to have azulejo
compile and install its binary dependencies,
you will need compilers, make
, and cmake
and standard headers
for zlib
and bz2
. All linux systems configured for development will have
these available. We test compilation under gcc version 10.2 on linux and
clang 12.0.0 on MacOS. We use program-guided optimization for one of the
binary dependencies, and we believe that gcc 10 does a much better job
of optimization than gcc 9, so it may benefit you to upgrade your compiler
if needed.
Once the prerequisite has been met, you may then install azulejo
in its own virtual environment by issuing the command:
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)"
If you are using zsh
, simply replace source_bash
in the above command line
with source_zsh
.
You may next proceed with installing binary dependencies.
azulejo
recognizes the following environmental variables:
- AZULEJO_INSTALL_DIR
- This is a writable directory for installation of binary dependencies. Binaries
will go into the
bin
directory. The default is the virtual environment directory. - BUILD_DEV
- This is the directory used for building binary dependencies. Default is the first memory device found for linux (e.g., /run/shm) or /tmp for MacOS. Set this if compilation fails because it runs out of memory.
- SCRATCH_DEV
- This is the directory used for temporary merging of lists. The default is /tmp, but you may set it to a fast memory based device if you have enough memory.
- MAKEOPTS
- These are the arguments to the
make
andmake install
commands when building dependencies. It's good to set this to the number of processors on your system before installing required dependencies. This variable is only used duringazulejo install
. - SPINNER_UPDATE_PERIOD
- This is the number of seconds between updates of the spinner. This defaults to 1, but it is advisable to set it higher for automated testing so as not to exceed logfile character limits.
- LOG_TO_PRINT
- If set to a log level such as
info
, the logger will be a simple print without using the more complex functions ofloguru
such as colors and logging to files. This is sometimes useful in automated testing.
In addition the optional dagchainer-tool
subcommand recognizes the
some environmental variables which can be shown via the command
azulejo dagchainer-tool --help
.
azulejo
requires MMseqs
for homology clustering and MUSCLE
for sequence alignment and initial tree-building.
azulejo
installs binaries into the virtualenv by default, so
any systemwide installations of these packages will not get clobbered by the install.
In particular, muscle
is PGO-optimized, which gives nearly a factor of 2 higher
performance than prebuilt binaries. For fastest installation, We recommand you set
MAKEOPTS
and install all required dependencies via the commands:
export MAKEOPTS=$(python -c 'import multiprocessing as mp; print(mp.cpu_count())') azulejo install all
There are three optional dependencies that can be installed via azulejo install
that are of interest only to a small subset of users who wish to compare against
other homology clustering and synteny methods.
usearch
is a licensed homology clustering program that is free for individual, non-commercial
use that can be downloaded and installed by the azulejo install usearch
command after accepting the license terms. azulejo install dagchainer-tool
gets you
a somewhat crude Bash script that uses BLAST homology clustering followed by
synteny calculation via DAGchainer.
dagchainer-tool
will need the dependency of perl
with bioperl
installed.
dagchainer_tool
increases the sequence ID length as part of its processing, so
if any of your sequence IDS are longer than about 30 characters, they will violate BLAST's
hard limit of 50 characters in sequence ID fields. In that case you will need
to install a patched version of BLAST using the command azulejo install blast-longids
.
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/joelb123/azulejo.git
Change to the azulejo/
directory and install with poetry:
poetry install -v
Run azulejo
with poetry
:
poetry run azulejo
Installation puts a single script called azulejo
in your path. The usage format is:
azulejo [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS][ARGS]
azulejo
uses a configuration file in TOML
format as the master input that associates files with phylogeny. The format of this file
is the familiar headings in square brackets followed by configuration values:
[glycines] rank = "genus" name = "Glycine" [glycines.glyso] rank = "species" name = "Glycine soja" [glycines.glyso.PI483463] rank = "strain" gff = "glyso.PI483463.gnm1.ann1.3Q3Q.gene_models_main.gff3.gz" fasta = "glyso.PI483463.gnm1.ann1.3Q3Q.protein_primaryTranscript.faa.gz" uri = "https://v1.legumefederation.org/data/index/public/Glycine_soja/PI483463.gnm1.ann1.3Q3Q/" comments = """ Glycine soja accession PI 483463 has been identified as being unusually salt-tolerant (Lee et al., 2009)."""
- [headings]
- There can be only one top-level heading, and that will be the name of the resulting output set. This name will be the name of an output directory that will be created in the current working directory, so this heading (and all subheadings) must obey UNIX filesystem naming rules or an error will result. Each heading level (indicated by a ".") will result in another taxonomic level and another directory level in the output directory. Depths do not need to be consistent.
- rank
- Each level defined must have a
rank
defined, and that rank must match one of the taxonomic ranks defined byazulejo
, which you can view and test using thecheck-taxonomic-rank
command. There are 24 major taxonomic ranks, each of which may be modified by 16 different prefixes for a total of 174 taxonomic levels (some of which are synonoymous).
- name
- Each level may (and usually should) have a
name
defined. This name is intended to be human-readable with no restrictions on the characters used, but it goes into plot legends in places, so it's best to not make it too long. If the name is not specified, it will be taken from the level name enclosed in single quotes (e.g., 'PI483463' for the example above).
- fasta
- If the level specifies a genome, it must have a
fasta
entry corresponding to the name of the protein FASTA file. In eukaryotes, the FASTA file should be a file of primary (generally longest) protein transcripts, if available, rather than all protein transcripts (i.e., not including splice variants). Sequences will be cleaned of dashes, stops, and other out-of-alphabet characters. Ambiguous residues at the beginnings and ends of sequences will be trimmed. Zero-length sequences will be discarded, which can result in a smaller number of sequences out. These files may be compressed, with extensions.gz
or.bz2
.
- gff
- If the level specifies a genome, it must have a
gff
entry corresponding to a version 3 Genome Feature File (GFF3) containingCDS
entries with ID values matching those IDs in the FASTA file. The same compression extensions as forfasta
entries apply. If theSOURCE
fields in those CDS entries (which contain the names of the DNA fragments such as scaffolds that the CDS came from) contain dot-separated components, those components that are identical across the entire file will be discarded by default. There is an opportunity later in the process to remap DNA source names to a common dictionary for comparison among chromosomes and plastids.
- uri
- This optional field may contain a a uniform resource identifier such as
https://sitename/dir/
.azulejo
uses smart-open for doing transparent on-the-fly decompression from a variety of file systems including HTTPS, HDFS, SSH, and SFTP (but not FTP). If this field is not supplied, local file access is assumed with paths relative to the current working directory. The URI will be prepended tofasta
andgff
paths, allowing for convenient downloading on-the-fly from sites such as LegumeInfo or GenBank. Downloads are not cached, so if you intend to runazulejo
multiple times on the same input data, you will save time by downloading and uncompressing files to local storage.
- preference
- This optional field may be used to override the genome preference heuristic that is the fall-thru preference after proxy-gene heuristics have been applied. This is an integer value, with lower integers getting the highest priority. Set this value to zero if you know in advance that one of the input genomes is considered the reference genome and, all things being equal, you would prefer to select proxy genes from this genome. You may also set these preference values later, after the default genome preference (genomes will be preferred in order of the most genes in a single DNA fragment) has already been applied, but before proxy gene selection.
- other info
- A design goal for
azulejo
was to not lose metadata, even if it was not used byazulejo
itself, while keeping metadata out of file names. As an aid in that goal, for each (sub)heading level/output directory,azulejo
creates a JSON file namednode_properties.json
at each node in the output hierarchy that containing all information from this file as well as other information calculated at ingestion time byazulejo
. You may specify any additional data you would like to pass along (e.g., for later use in a web page) and it will be translated from TOML to JSON and passed along, such as the multi-linecomments
field in the example. Examples of useful metadata that may be easier to enter at ingestion time than to garner later include taxon IDs of the level and its parent, common names, URLs of papers describing the genome, and geographic origin of the sample.
A copy of the input file will be saved in the output directory under the name input.toml
.
See the examples in the tests/testdata
repository directory for examples of input data.
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). |
A listing of commands is available via azulejo --help
.
The currently implemented commands are, in the order they will normally be run:
install | Check for/install binary dependencies. |
ingest | Marshal protein and genome sequence information. |
homology | Calculate homology clusters, MSAs, trees. |
synteny | Calculate synteny anchors. |
proxy-genes | Calculate a set of proxy genes from synteny files. |
parquet-to-tsv | Reads parquet file, writes tsv. |
azulejo
stores most intermediate results in the Parquet format with
extension .parq
. These binary files are compressed and typically can
be read more than 30X faster than the tab-separated-value (TSV) files they
can be interconverted with. In addition, Parquet files do not lose metadata
such as binary representation sizes.
Each command has its COMMANDOPTIONS
, which may be listed with:
azulejo COMMAND --help
Latest Release | ||
Activity | ||
Downloads | ||
Download Rate | ||
License | ||
Code Grade | ||
Coverage | ||
Build | ||
Issues | ||
Code Style |