Package: asmc-preparedecoding
ASMC Prepare DecodingTool to compute decoding quantities.QuickstartInstall the Python module from PyPIMost functionality is available through a Python module which can be installed with:pipinstallasmc-preparedecodingThis Python module is currently available on Linux and macOS.
We hope it will be available soon on Windows.Example notebookExamples for using the Python module can be found in the following Jupyter notebook:creating decoding quantitiesPlease note that to run the notebook you should first clone the repository and install Jupyter:gitclonehttps://github.com/PalamaraLab/PrepareDecoding.gitcdPrepareDecoding

pipinstalljupyter
jupyter-notebooknotebooks/CreatingDecodingQuantities.ipynbAPI documentationA description of the API can be found here:api docsFile formatsDescriptions of the file formats used can be found here:file formatsLicenseThis project is currently released under the GNU General Public License Version 3.Release Notesv2.2.3 (2023-02-22)Infrastructure updates and building wheels for newer Python versions.
No change in functionality.v2.2.2 (2021-09-28)Improved documentation, now availablehere.
No change in functionality.v2.2.1 (2021-09-01)Very minor fix to links in documentation.
No change in functionality.v2.2 (2021-09-01)You can now specify discretizations in the following manner:as a file:discretization='/path/to/discretization.disc'(existing functionality)as a number of quantiles, which will be calculated at runtime:discretization=[100]as a number of pre-specified quantiles plus a number of additional quantiles calculated at runtime:discretization=[[30.0, 12], [100.0, 15], 39]this will create 12 discretization points at a spacing of 30.0 (starting from 0.0), followed by 15 at a spacing of 100, followed by 39 additional quantilesYou can now specify built-in frequencies information. Currently, the only supported frequencies are from UKBB. Frequencies can now be specified in the following manner:as a file:frequencies='/path/to/frequencies.frq'(existing functionality)as a string:frequencies='UKBB'Breaking changesThe Python API has been simplified, and the strong types mentioned in the v2.1 release are no longer required in Python.
Please see the Jupyter Notebook for examples of the current API.The strong types remain in the C++ API.
Please see the fileTestPrepareDecoding.cppfor examples of the C++ library API.There is now a single top-level methodprepare_decoding(Python) andprepareDecoding(C++).
If the CSFS file parameter is a valid file, CSFS will be loaded from file.
If the CSFS file parameter is an empty string, CSFS will be calculated at runtime.Other changesVarious other minor changes have been made.v2.1 (2021-05-13)Default demographies are now bundled with Prepare Decoding.
You can now either supply your own demography file, or choose from the following default demographies:ACB, ASW, BEB, CDX, CEU, CHB, CHS, CLM, ESN, FIN, GBR, GIH, GWD, IBS, ITU, JPT, KHV, LWK, MSL, MXL, PEL, PJL, PUR, STU, TSI, YRIBreaking changesWhen using the C++ or Python libraries, methods that previous specified a demography file as a string now require an instance of a lightweight strong typeDemography:In C++, to specify a file:Demography d("/path/to/demography.demo");In C++, to specify a default:Demography d("CEU");In Python, to specify a file:d = Demography('/path/to/demography.demo')In C++, to specify a default:d = Demography('CEU')A default-constructed Demography will use the default CEU.Other changesNonev2.0 (2021-04-22)Computing CSFS values is now bundled with this project, and no longer relies on the optionalsmcppdependency.Breaking changesPython methodcreate_from_precomputed_csfsis renamedprepare_decoding_precalculated_csfs, but it behaves identically.Python methodcreate_from_scratchis renamedcalculate_csfs_and_prepare_decoding, and no longer requires the Python packagesmcpp.Other changesSome floating point numbers in output files are now written with higher precision.v1.1 (2021-03-19)Minor fixes.Breaking changesNoneOther changesPython wheels now also built for Windows as well as macOS and Linux.Corrected syntax in package README.v1.0 (2021-03-18)First public release of ASMC Prepare Decoding, with functionality as described and used inthese notebooks.