High performance phylogenetic diversity calculations
Project description
UniFrac
Canonically pronounced yew-nih-frak
The de facto repository for high-performance phylogenetic diversity calculations. The methods in this repository are based on an implementation of the Strided State UniFrac algorithm which is faster, and uses less memory than Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in both double and single precision (fp32). This repository also includes Stacked Faith (manuscript in preparation), a method for calculating Faith's PD that is faster and uses less memory than the Fast UniFrac-based reference implementation.
This repository produces a C API exposed via a shared library which can be linked against by any programming language.
Citation
A detailed description of the Strided State UniFrac algorithm can be found in McDonald et al. 2018 Nature Methods. Please note that this package implements multiple UniFrac variants, which may have their own citation. Details can be found in the help output from the command line interface in the citations section, and is included immediately below:
ssu
For UniFrac, please see:
McDonald et al. Nature Methods 2018; DOI: 10.1038/s41592-018-0187-8
Lozupone and Knight Appl Environ Microbiol 2005; DOI: 10.1128/AEM.71.12.8228-8235.2005
Lozupone et al. Appl Environ Microbiol 2007; DOI: 10.1128/AEM.01996-06
Hamady et al. ISME 2010; DOI: 10.1038/ismej.2009.97
Lozupone et al. ISME 2011; DOI: 10.1038/ismej.2010.133
For Generalized UniFrac, please see:
Chen et al. Bioinformatics 2012; DOI: 10.1093/bioinformatics/bts342
For Variance Adjusted UniFrac, please see:
Chang et al. BMC Bioinformatics 2011; DOI: 10.1186/1471-2105-12-118
faithpd
For Faith's PD, please see:
Faith Biological Conservation 1992; DOI: 10.1016/0006-3207(92)91201-3
Install
At this time, there are three primary ways to install the library. The first is through QIIME2, the second is through bioconda, and the third is via pip. It is also possible to clone the repository and install the C++ API with sucpp/Makefile or python bindings with setup.py.
Compilation has been performed on both LLVM 9.0.0 (OS X >= 10.12) or GCC 4.9.2 (Centos >= 6) and HDF5 >= 1.8.17. Python installation requires Python >= 3.5, NumPy >= 1.12.1, scikit-bio >= 0.5.1, and Cython >= 0.28.3.
Installation time should be a few minutes at most.
Install (QIIME2)
The easiest way to use this library is through QIIME2. This library is installed by default with the QIIME 2 Core Distribution. Currently, this module is used for phylogenetic diversity calculations in qiime diversity beta-phylogenetic for UniFrac and qiime diversity alpha-phylogenetic-alt for Faith's PD.
Install (bioconda)
This library can also be installed via a combination of conda-forge and bioconda:
conda create --name unifrac -c conda-forge -c bioconda unifrac
Note: Only the CPU version of the binaries is currently available in conda. The GPU version must either be locally compiled using freely-available NVIDIA HPC SDK or obtained from a github branch.
Note: If you desire a fully optimized the binaries for your CPU, you can compile them locally.
Install (pip)
pip install unifrac
Install (native)
To install, first the binary needs to be compiled. This assumes that the HDF5 toolchain and libraries are available. More information about how to setup the stack can be found here.
Assuming h5c++ is in your path, the following should work:
pip install -e .
Note: if you are using conda we recommend installing HDF5 using the
conda-forge channel, for example:
conda install -c conda-forge hdf5
Examples of use
Below are a few light examples of different ways to use this library.
QIIME2
To use Strided State UniFrac through QIIME2, you need to provide a FeatureTable[Frequency] and a Phylogeny[Rooted] artifacts. An example of use is:
qiime diversity beta-phylogenetic --i-table table-evenly-sampled.qza \
--i-phylogeny a-tree.qza \
--o-distance-matrix resulting-distance-matrix.qza \
--p-metric unweighted_unifrac
To use Stacked Faith through QIIME2, given similar artifacts, you can use:
qiime diversity alpha-phylogenetic-alt --i-table table-evenly-sampled.qza \
--i-phylogeny a-tree.qza \
--o-alpha-diversity resulting-diversity-series.qza \
--p-metric faith_Pd
Python
The library can be accessed directly from within Python. If operating in this mode, the API methods are expecting a filepath to a BIOM-Format V2.1.0 table, and a filepath to a Newick formatted phylogeny.
$ python
Python 3.7.8 | packaged by conda-forge | (default, Nov 27 2020, 19:24:58)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import unifrac
>>> dir(unifrac)
['__all__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__',
'__package__', '__path__', '__spec__', '__version__', '_api', '_meta', '_methods',
'faith_pd',
'generalized', 'generalized_fp32', 'generalized_fp32_to_file', 'generalized_to_file',
'h5pcoa', 'h5unifrac', 'meta', 'pkg_resources', 'ssu', 'ssu_to_file',
'unweighted', 'unweighted_fp32', 'unweighted_fp32_to_file', 'unweighted_to_file',
'weighted_normalized', 'weighted_normalized_fp32', 'weighted_normalized_fp32_to_file', 'weighted_normalized_to_file',
'weighted_unnormalized', 'weighted_unnormalized_fp32', 'weighted_unnormalized_fp32_to_file', 'weighted_unnormalized_to_file']
>>> print(unifrac.unweighted_fp32.__doc__)
Compute Unweighted UniFrac using fp32 math
Parameters
----------
table : str
A filepath to a BIOM-Format 2.1 file.
phylogeny : str
A filepath to a Newick formatted tree.
threads : int, optional
The number of threads to split it into. Default of 1.
variance_adjusted : bool, optional
Adjust for varianace or not. Default is False.
bypass_tips : bool, optional
Bypass the tips of the tree in the computation. This reduces compute
by about 50%, but is an approximation.
Returns
-------
skbio.DistanceMatrix
The resulting distance matrix.
Raises
------
IOError
If the tree file is not found
If the table is not found
ValueError
If the table does not appear to be BIOM-Format v2.1.
If the phylogeny does not appear to be in Newick format.
Notes
-----
Unweighted UniFrac was originally described in [1]_. Variance Adjusted
UniFrac was originally described in [2]_, and while its application to
Unweighted UniFrac was not described, factoring in the variance adjustment
is still feasible and so it is exposed.
References
----------
.. [1] Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for
comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235
(2005).
.. [2] Chang, Q., Luan, Y. & Sun, F. Variance adjusted weighted UniFrac: a
powerful beta diversity measure for comparing communities based on
phylogeny. BMC Bioinformatics 12:118 (2011).
>>> print(unifrac.unweighted_fp32_to_file.__doc__)
Compute Unweighted UniFrac using fp32 math and write to file
Parameters
----------
table : str
A filepath to a BIOM-Format 2.1 file.
phylogeny : str
A filepath to a Newick formatted tree.
out_filename : str
A filepath to the output file.
pcoa_dims : int, optional
Number of dimensions to use for PCoA compute.
if set to 0, no PCoA is computed.
Defaults of 10.
threads : int, optional
The number of threads to split it into. Default of 1.
variance_adjusted : bool, optional
Adjust for varianace or not. Default is False.
bypass_tips : bool, optional
Bypass the tips of the tree in the computation. This reduces compute
by about 50%, but is an approximation.
format : str, optional
Output format to use. Defaults to "hdf5".
buf_dirname : str, optional
If set, the directory where the disk buffer is hosted,
can be used to reduce the amount of memory needed.
Returns
-------
str
A filepath to the output file.
Raises
------
IOError
If the tree file is not found
If the table is not found
If the output file cannot be created
ValueError
If the table does not appear to be BIOM-Format v2.1.
If the phylogeny does not appear to be in Newick format.
Notes
-----
Unweighted UniFrac was originally described in [1]_. Variance Adjusted
UniFrac was originally described in [2]_, and while its application to
Unweighted UniFrac was not described, factoring in the variance adjustment
is still feasible and so it is exposed.
References
----------
.. [1] Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for
comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235
(2005).
.. [2] Chang, Q., Luan, Y. & Sun, F. Variance adjusted weighted UniFrac: a
powerful beta diversity measure for comparing communities based on
phylogeny. BMC Bioinformatics 12:118 (2011).
>>> print(unifrac.h5unifrac.__doc__)
Read UniFrac from a hdf5 file
Parameters
----------
h5file : str
A filepath to a hdf5 file.
Returns
-------
skbio.DistanceMatrix
The distance matrix.
Raises
------
OSError
If the hdf5 file is not found
KeyError
If the hdf5 does not have the necessary fields
References
----------
.. [1] Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for
comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235
(2005).
.. [2] Chang, Q., Luan, Y. & Sun, F. Variance adjusted weighted UniFrac: a
powerful beta diversity measure for comparing communities based on
phylogeny. BMC Bioinformatics 12:118 (2011).
>>> print(unifrac.faith_pd.__doc__)
Execute a call to the Stacked Faith API in the UniFrac package
Parameters
----------
biom_filename : str
A filepath to a BIOM 2.1 formatted table (HDF5)
tree_filename : str
A filepath to a Newick formatted tree
Returns
-------
pd.Series
Series of Faith's PD for each sample in `biom_filename`
Raises
------
IOError
If the tree file is not found
If the table is not found
If the table is empty
Command line
The methods can also be used directly through the command line after install:
$ which ssu
/Users/<username>/miniconda3/envs/qiime2-20xx.x/bin/ssu
$ ssu --help
usage: ssu -i <biom> -o <out.dm> -m [METHOD] -t <newick> [-n threads] [-a alpha] [-f] [--vaw]
[--mode [MODE]] [--start starting-stripe] [--stop stopping-stripe] [--partial-pattern <glob>]
[--n-partials number_of_partitions] [--report-bare] [--format|-r out-mode]
-i The input BIOM table.
-t The input phylogeny in newick.
-m The method, [unweighted | weighted_normalized | weighted_unnormalized | generalized |
unweighted_fp32 | weighted_normalized_fp32 | weighted_unnormalized_fp32 | generalized_fp32].
-o The output distance matrix.
-n [OPTIONAL] The number of threads, default is 1.
-a [OPTIONAL] Generalized UniFrac alpha, default is 1.
-f [OPTIONAL] Bypass tips, reduces compute by about 50%.
--vaw [OPTIONAL] Variance adjusted, default is to not adjust for variance.
--mode [OPTIONAL] Mode of operation:
one-off : [DEFAULT] compute UniFrac.
partial : Compute UniFrac over a subset of stripes.
partial-report : Start and stop suggestions for partial compute.
merge-partial : Merge partial UniFrac results.
--start [OPTIONAL] If mode==partial, the starting stripe.
--stop [OPTIONAL] If mode==partial, the stopping stripe.
--partial-pattern [OPTIONAL] If mode==merge-partial, a glob pattern for partial outputs to merge.
--n-partials [OPTIONAL] If mode==partial-report, the number of partitions to compute.
--report-bare [OPTIONAL] If mode==partial-report, produce barebones output.
--format|-r [OPTIONAL] Output format:
ascii : [DEFAULT] Original ASCII format.
hfd5 : HFD5 format. May be fp32 or fp64, depending on method.
hdf5_fp32 : HFD5 format, using fp32 precision.
hdf5_fp64 : HFD5 format, using fp64 precision.
--pcoa [OPTIONAL] Number of PCoA dimensions to compute (default: 10, do not compute if 0)
--diskbuf [OPTIONAL] Use a disk buffer to reduce memory footprint. Provide path to a fast partition (ideally NVMe).
Citations:
For UniFrac, please see:
McDonald et al. Nature Methods 2018; DOI: 10.1038/s41592-018-0187-8
Lozupone and Knight Appl Environ Microbiol 2005; DOI: 10.1128/AEM.71.12.8228-8235.2005
Lozupone et al. Appl Environ Microbiol 2007; DOI: 10.1128/AEM.01996-06
Hamady et al. ISME 2010; DOI: 10.1038/ismej.2009.97
Lozupone et al. ISME 2011; DOI: 10.1038/ismej.2010.133
For Generalized UniFrac, please see:
Chen et al. Bioinformatics 2012; DOI: 10.1093/bioinformatics/bts342
For Variance Adjusted UniFrac, please see:
Chang et al. BMC Bioinformatics 2011; DOI: 10.1186/1471-2105-12-118
$ which faithpd
/Users/<username>/miniconda3/envs/qiime2-20xx.x/bin/faithpd
$ faithpd --help
usage: faithpd -i <biom> -t <newick> -o <out.txt>
-i The input BIOM table.
-t The input phylogeny in newick.
-o The output series.
Citations:
For Faith's PD, please see:
Faith Biological Conservation 1992; DOI: 10.1016/0006-3207(92)91201-3
Shared library access
In addition to the above methods to access UniFrac, it is also possible to link against the shared library. The C API is described in sucpp/api.hpp, and examples of linking against this API can be found in examples/.
Minor test dataset
A small test .biom and .tre can be found in sucpp/. An example with expected output is below, and should execute in 10s of milliseconds:
$ ssu -i sucpp/test.biom -t sucpp/test.tre -m unweighted -o test.out
$ cat test.out
Sample1 Sample2 Sample3 Sample4 Sample5 Sample6
Sample1 0 0.2 0.5714285714285714 0.6 0.5 0.2
Sample2 0.2 0 0.4285714285714285 0.6666666666666666 0.6 0.3333333333333333
Sample3 0.5714285714285714 0.4285714285714285 0 0.7142857142857143 0.8571428571428571 0.4285714285714285
Sample4 0.6 0.6666666666666666 0.7142857142857143 0 0.3333333333333333 0.4
Sample5 0.5 0.6 0.8571428571428571 0.3333333333333333 0 0.6
Sample6 0.2 0.3333333333333333 0.4285714285714285 0.4 0.6 0
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
