PyOMADB is a python client to the OMA browser, using the REST API. As such, it requires a stable internet connection to operate. We also provide a similar wrapper for R (https://github.com/DessimozLab/omadb).
Documentation is available here. A notebook containing examples of how to use the package is available here.
New (version 2.1.0) - in order to facilitate the functional and evolutionary aspects of coronaviruses, the new Corona OMA Browser has been launched. Please see the Corona-OMA Example for more information.
If you use our package in your work, please consider citing:
Kaleb K, Warwick Vesztrocy A, Altenhoff A and Dessimoz C. Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. F1000Research 2019, 8:42 (https://doi.org/10.12688/f1000research.17548.1)
The package requires Python 3 (>=3.6). The easiest way to install is using pip, to install the package from PyPI.
pip install omadb
Documentation is available here.
As an example, if a user has the ID of their gene of interest, they can find the corresponding OMA entry as follows:
from omadb import Client
c = Client()
prot_id = 'P53_RAT'
r = c.proteins[prot_id] # Can also be called as c.proteins.info(prot_id)
This is then a Python dictionary containing information about this entry. Some information is lazily loaded, for example:
orth = r.orthologs # Will lazily load in the background.
Alternatively, if the user has the sequence but no ID, the closest entry in OMA can be identified as so:
seq = 'MKLVFLVLLFLGALGLCLAGRRRSVQWCAVSQPEATKCFQWQRNMRKVRGPPVSCIKRDSPIQCIQAIAENRADAVTLDGGFIYEAGLAPYKLRPVAAEVYGTERQPRTHYYAVAVVKKGGSFQLNELQGLKSCHTGLRRTAGWNVPIGTLRPFLNWTGPPEPIEAAVARFFSASCVPGADKGQFPNLCRLCAGTGENKCAFSSQEPYFSYSGAFKCLRDGAGDVAFIRESTVFEDLSDEAERDEYELLCPDNTRKPVDKFKDCHLARVPSHAVVARSVNGKEDAIWNLLRQAQEKFGKDKSPKFQLFGSPSGQKDLLFKDSAIGFSRVPPRIDSGLYLGSGYFTAIQNLRKSEEEVAARRARVVWCAVGEQELRKCNQWSGLSEGSVTCSSASTTEDCIALVLKGEADAMSLDGGYVYTAGKCGLVPVLAENYKSQQSSDPDPNCVDRPVEGYLAVAVVRRSDTSLTWNSVKGKKSCHTAVDRTAGWNIPMGLLFNQTGSCKFDEYFSQSCAPGSDPRSNLCALCIGDEQGENKCVPNSNERYYGYTGAFRCLAENAGDVAFVKDVTVLQNTDGNNNEAWAKDLKLADFALLCLDGKRKPVTEARSCHLAMAPNHAVVSRMDKVERLKQVLLHQQAKFGRNGSDCPDKFCLFQSETKNLLFNDNTECLARLHGKTTYEKYLGPQYVAGITNLKKCSTSPLLEACEFLRK'
r = c.proteins.search(seq)
For further examples that correspond to the R versions given in the paper, see the Jupyter notebook, which is also available on mybinder.
In order to facilitate the functional and evolutionary aspects of coronaviruses, the new Corona OMA Browser has been launched.
The endpoint for the Corona OMA Browser is corona.omabrowser.org/api and can be used in PyOMADB by importing CoronaClient instead of Client.
from omadb import CoronaClient
c = CoronaClient() # Connects to Corona OMA endpoint
prot_id = 'R1AB_SARS2' # Severe acute respiratory syndrome coronavirus 2
r = c.proteins[prot_id] # Can also be called as c.proteins.info(prot_id)
This is then a Python dictionary containing information about this entry. Some information is lazily loaded, for example:
orth = r.orthologs # Will lazily load in the background.
PyOMADB is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
PyOMADB is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with PyOMADB. If not, see http://www.gnu.org/licenses/.