HogProf 0.0.11

Phylogenetic Profiling with OMA and minhashing

HogProf

• HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient.
• Still under major development and may change

Features

• Using orthoxoml files and a taxonomy calculated enhanced phylogenies of each family
• These are transformed into minhash signatures and a locally sensitive hashing forest object for search and comparison of profiles
• Taxonomic levels and evolutionary event types ( presence, loss, duplication ) can have custom weight in profile construction
• Optimization of weights using machine learning

If you run into any problems feel free to contact me at [e-mail]

Quickstart

to install from github

$ git clone https://github.com/DessimozLab/HogProf.git
$ pip install -r pipreqs.txt .

or to install from pypi

$ pip install hogprof

lets get a current version of the OMA hdf5 file and GAF. This will alow us to use the HOGs and study the functional enrichment of our search results.

$ cd ../..
$ mkdir YourOmaDirectory
$ cd YourOmaDirectory
$ wget https://omabrowser.org/All/OmaServer.h5
$ wget https://omabrowser.org/All/oma-go.txt.gz

We also need to make a location to store our pyprofiler databases

$ cd ..
$ mkdir YourHogProfDirectory

Ok. We're ready! Now let's compile a database containing all HOGs and our desired taxonomic levels using default settings. Launch the lshbuilder. dbtypes available on the command line are : all , plants , archaea, bacteria , eukarya , protists , fungi , metazoa and vertebrates. These will use the NCBI taxonomy as a tree to annotate events in different gene family's histories.

If you are using an OMA release before 2022 you will need to use the NCBI tree. This is the default tree used by HogProf.

$python lshbuilder.py --outpath YourHogProfDirectory --dbtype all --OMA YourOmaDirectory/OmaServer.h5 --nthreads numberOfCPUcores         

If you are using OMA releases after 2022 we will also be downloading the OMA taxonomic tree since it is more accurate than the NCBI tree. This will be used to annotate the events in the gene family histories.

wget https://omabrowser.org/All/speciestree.nwk

Ok now we're ready to use the OMA tree to build our database.

$python lshbuilder.py --outpath YourHogProfDirectory --dbtype all --OMA YourOmaDirectory/OmaServer.h5 --nthreads numberOfCPUcores --mastertree YourOmaDirectory/speciestree.nwk --reformat_names True

This should build a taxonomic tree for the genomes contained in the release and then calculate enhanced phylogenies for all HOGs in OMA.

Once the database is completed it can be interogated using a profiler object. Construction and usage of this object should be done using a python script or notebook. This shown in the example notebook searchenrich.ipynb found in the examples. Please feel free to modify it to suit the needs of your own research.