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PyOMADB

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.

Binder

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.

Citation

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)

Installation

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

Documentation is available here.

Example

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.

Corona-OMA Example

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.

License

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/.

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PyOMADB is a python client to the OMA browser, using the REST API.

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