diff --git a/.gitattributes b/.gitattributes index a6344aac8c09253b3b630fb776ae94478aa0275b..553cbccd3943bbf5af13c6f492de30490b56101c 100644 --- a/.gitattributes +++ b/.gitattributes @@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text *.zip filter=lfs diff=lfs merge=lfs -text *.zst filter=lfs diff=lfs merge=lfs -text *tfevents* filter=lfs diff=lfs merge=lfs -text +genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..b6e47617de110dea7ca47e087ff1347cc2646eda --- /dev/null +++ b/.gitignore @@ -0,0 +1,129 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000000000000000000000000000000000000..c2b4bbb5ecae843c7a8bad6dad73969f0b94d07a --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,3 @@ +include README.md +include genet-models/DeepPrime_FT/* + diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..a6fd05dc12a8cd433b86a79b8a060a2c0d42de29 --- /dev/null +++ b/README.md @@ -0,0 +1,13 @@ +# genet-models +prediction models for genet + +# Available models +The DeepSpCas9 model predicts the activity of SpCas9. It is based on the model presented in the 2019 Sci.Adv. publication. + +# DeepSpCas9-variants +The DeepSpCas9-variants model predicts the activity of various SpCas9 PAM variants. + +# DeepPrime / DeepPrime-FT +These models predict the efficiency of Prime editing. They are based on the models from the 2023 Cell paper. + +Original author: Goosang-Yu ~ https://github.com/Goosang-Yu/genet-models \ No newline at end of file diff --git a/genet_models/DeepPrime/DP_variant_293T_NRCH-PE2max_Opti_220815/dp_mean.csv b/genet_models/DeepPrime/DP_variant_293T_NRCH-PE2max_Opti_220815/dp_mean.csv new file mode 100644 index 0000000000000000000000000000000000000000..3d5fe51bf89554d8fcf666d29472cdfb666899fe --- /dev/null +++ b/genet_models/DeepPrime/DP_variant_293T_NRCH-PE2max_Opti_220815/dp_mean.csv @@ -0,0 +1 @@ +1.278571736678127 \ No newline at end of file diff --git a/genet_models/DeepPrime/DP_variant_293T_NRCH-PE2max_Opti_220815/dp_std.csv b/genet_models/DeepPrime/DP_variant_293T_NRCH-PE2max_Opti_220815/dp_std.csv new file mode 100644 index 0000000000000000000000000000000000000000..9dd80a0fe2565424eff48643f106569ecdbf6b33 --- /dev/null +++ b/genet_models/DeepPrime/DP_variant_293T_NRCH-PE2max_Opti_220815/dp_std.csv @@ -0,0 +1 @@ +4.166661527112254 \ No 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+TmD,86.99805021317079 +nGCcnt1,2.7732525503627192 +nGCcnt2,5.33836986654092 +nGCcnt3,5.78118287683824 +fGCcont1,19.879753110769244 +fGCcont2,13.667914440222775 +fGCcont3,11.724377914018946 +MFE3,3.9928788684309544 +MFE4,2.111348540438727 +DeepSpCas9_score,18.133562777346093 diff --git a/genet_models/DeepPrime/DeepPrime_off/final_model_0.pt b/genet_models/DeepPrime/DeepPrime_off/final_model_0.pt new file mode 100644 index 0000000000000000000000000000000000000000..7ecb71280ee161cfb0e46131aa290559179fb523 --- /dev/null +++ b/genet_models/DeepPrime/DeepPrime_off/final_model_0.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8e040440818b68e0a1b01ef17e654763ba1f16fe40a521690698d6aefe14ae84 +size 1380013 diff --git a/genet_models/DeepPrime/DeepPrime_off/final_model_1.pt b/genet_models/DeepPrime/DeepPrime_off/final_model_1.pt new file mode 100644 index 0000000000000000000000000000000000000000..1788be548c9aa5448fc2291216dc9334c71f916a --- /dev/null +++ b/genet_models/DeepPrime/DeepPrime_off/final_model_1.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:16bab4b795957d19b4d47dc5c740136739f69de087d052b7381573d3f49099f1 +size 1380013 diff --git a/genet_models/DeepPrime/DeepPrime_off/final_model_2.pt b/genet_models/DeepPrime/DeepPrime_off/final_model_2.pt new file mode 100644 index 0000000000000000000000000000000000000000..b2a19e4a056dd92a24ef1869cd5be37f16a85d76 --- /dev/null +++ b/genet_models/DeepPrime/DeepPrime_off/final_model_2.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0ed6fc32817e25d362b34ec18bda05b4b17b14662562069a396e035a7282bf74 +size 1380013 diff --git a/genet_models/DeepPrime/DeepPrime_off/final_model_3.pt b/genet_models/DeepPrime/DeepPrime_off/final_model_3.pt new file mode 100644 index 0000000000000000000000000000000000000000..6aa7e7a8e5c5025236f2b05b98e3efc145cc2a1b --- /dev/null +++ b/genet_models/DeepPrime/DeepPrime_off/final_model_3.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:95e2fc9a85ec9b98e347a473c8876e56ab909999a922ff7c058f2f87bbc35822 +size 1380013 diff --git a/genet_models/DeepPrime/DeepPrime_off/final_model_4.pt b/genet_models/DeepPrime/DeepPrime_off/final_model_4.pt new file mode 100644 index 0000000000000000000000000000000000000000..c9e163be877a382d825b8a203df08c6922d8d306 --- /dev/null +++ b/genet_models/DeepPrime/DeepPrime_off/final_model_4.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3ccdc9f3156eb56bffee23190f198440c3517b1cc79dd83a8afbbfefb820ff18 +size 1380013 diff --git a/genet_models/DeepPrime/DeepPrime_off/mean.csv b/genet_models/DeepPrime/DeepPrime_off/mean.csv new file mode 100644 index 0000000000000000000000000000000000000000..70e07ec5f0ea29099389e54c61a417bed3e0d229 --- /dev/null +++ b/genet_models/DeepPrime/DeepPrime_off/mean.csv @@ -0,0 +1,24 @@ +PBSlen,9.760297795390713 +RTlen,21.59864953253049 +RT-PBSlen,31.358947327921204 +Edit_pos,12.03467354084106 +Edit_len,1.2414412681312763 +RHA_len,9.573348466776961 +type_sub,0.5325612712092648 +type_ins,0.28419452887537994 +type_del,0.18324419991535532 +Tm1,-1.6020357759180939 +Tm2,46.53187477512031 +Tm2new,45.83593072237111 +Tm3,-351.4090675969776 +Tm4,49.164981905259324 +TmD,-397.9409424069532 +nGCcnt1,5.169350929167789 +nGCcnt2,11.965676580354739 +nGCcnt3,17.135027509522526 +fGCcont1,53.24942701319918 +fGCcont2,56.96251270065411 +fGCcont3,55.35720054318455 +MFE3,-5.062673233042171 +MFE4,-2.0235566157515863 +DeepSpCas9_score,41.752208346838835 diff --git a/genet_models/DeepPrime/DeepPrime_off/std.csv b/genet_models/DeepPrime/DeepPrime_off/std.csv new file mode 100644 index 0000000000000000000000000000000000000000..2e78eccb2e297db9aa34f0bd965c9ceb387563fc --- /dev/null +++ b/genet_models/DeepPrime/DeepPrime_off/std.csv @@ -0,0 +1,24 @@ +PBSlen,4.2779797145915035 +RTlen,9.58095013656761 +RT-PBSlen,9.770225369937926 +Edit_pos,7.856330180937928 +Edit_len,0.5419997466653621 +RHA_len,7.1441933870009695 +type_sub,0.4989395969581377 +type_ins,0.45103079863979245 +type_del,0.38686734024852837 +Tm1,73.01700817048199 +Tm2,32.23366468797141 +Tm2new,34.15977639082166 +Tm3,79.61333468825967 +Tm4,30.731834011924576 +TmD,86.99805021317079 +nGCcnt1,2.7732525503627192 +nGCcnt2,5.33836986654092 +nGCcnt3,5.78118287683824 +fGCcont1,19.879753110769244 +fGCcont2,13.667914440222775 +fGCcont3,11.724377914018946 +MFE3,3.9928788684309544 +MFE4,2.111348540438727 +DeepSpCas9_score,18.133562777346093 diff --git a/genet_models/DeepPrime/__init__.py b/genet_models/DeepPrime/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..d48a2e36564e90f30dd57767f12c855a7c3b6907 --- /dev/null +++ b/genet_models/DeepPrime/__init__.py @@ -0,0 +1 @@ +from genet_models import * \ No newline at end of file diff --git a/genet_models/DeepPrime/functional.py b/genet_models/DeepPrime/functional.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.data-00000-of-00001 b/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.data-00000-of-00001 new file mode 100644 index 0000000000000000000000000000000000000000..cc13c17ceb6759cd698ae6c2f98f51166f2345cb --- /dev/null +++ b/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.data-00000-of-00001 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bc126d09b761594fe3a4e800269ad7cbc4e4fd9bfe7254bec958caf7f527488f +size 2785580 diff --git a/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.index b/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.index new file mode 100644 index 0000000000000000000000000000000000000000..4229f0b59969c16e5f455fac82304ece54b9eef0 Binary files /dev/null and b/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.index differ diff --git a/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.meta b/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.meta new file mode 100644 index 0000000000000000000000000000000000000000..5c375182ecc647512f518f176b3b937de62d2c1b Binary files /dev/null and b/genet_models/DeepSpCas9/PreTrain-Final-3-5-7-100-70-40-0.001-550-80-60.meta differ diff --git a/genet_models/__init__.py b/genet_models/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..08176c913def4a323935da00f09369e1878ae293 --- /dev/null +++ b/genet_models/__init__.py @@ -0,0 +1,4 @@ +from genet_models.utils import __version__ +from genet_models.functional import * + +__all__ = ['__version__'] \ No newline at end of file diff --git a/genet_models/functional.py b/genet_models/functional.py new file mode 100644 index 0000000000000000000000000000000000000000..b619f15f69a4d4c5b950f77a0e3376b2642cd992 --- /dev/null +++ b/genet_models/functional.py @@ -0,0 +1,78 @@ +import os, sys, glob +import inspect + +from genet_models import DeepPrime + +''' +Model finder repo +Get your models from here! +''' + + +def load_genet_model(model_id='PE2', cell_type='HEK293T'): + ''' + model_id: PE2, PE2max, PE4max, PE2max-e, PE4max-e, NRCH_PE2, NRCH_PE2max, NRCH_PE4max + cell_rtpe: HEK293T, A549, DLD1, HCT116, HeLa, MDA-MB-231, NIH3T3 + + >>> from genet_models import load_model + >>> model_dir, model_type = load_model('PE2max', 'HEK293T') + + ''' + + print('get model: %s - %s' % (model_id, cell_type)) + + model_dir = inspect.getfile(DeepPrime).replace('/__init__.py', '').replace('\\__init__.py', '') + + dict_models = { + + 'HEK293T': { + 'PE2' : 'DeepPrime_base', + 'NRCH_PE2' : 'DP_variant_293T_NRCH_PE2_Opti_220428', + 'NRCH_PE2max': 'DP_variant_293T_NRCH-PE2max_Opti_220815', + 'PE2max' : 'DP_variant_293T_PE2max_Opti_220428', + 'PE2max-e' : 'DP_variant_293T_PE2max_epegRNA_Opti_220428', + 'PE4max' : 'DP_variant_293T_PE4max_Opti_220728', + 'PE4max-e' : 'DP_variant_293T_PE4max_epegRNA_Opti_220428', + }, + + 'A549': { + 'PE2max' : 'DP_variant_A549_PE2max_Opti_221114', + 'PE2max-e' : 'DP_variant_A549_PE2max_epegRNA_Opti_220428', + 'PE4max' : 'DP_variant_A549_PE4max_Opti_220728', + 'PE4max-e' : 'DP_variant_A549_PE4max_epegRNA_Opti_220428', + + }, + + 'DLD1': { + 'NRCH_PE4max': 'DP_variant_DLD1_NRCHPE4max_Opti_220728', + 'PE2max' : 'DP_variant_DLD1_PE2max_Opti_221114', + 'PE4max' : 'DP_variant_DLD1_PE4max_Opti_220728', + }, + + 'HCT116': { + 'PE2' : 'DP_variant_HCT116_PE2_Opti_220428', + }, + + 'HeLa': { + 'PE2max' : 'DP_variant_HeLa_PE2max_Opti_220815', + }, + + 'MDA-MB-231': { + 'PE2' : 'DP_variant_MDA_PE2_Opti_220428', + }, + + 'NIH3T3': { + 'NRCH_PE4max': 'DP_variant_NIH_NRCHPE4max_Opti_220815', + }, + + } + + + try: + model_type = dict_models[cell_type][model_id] + except: + print('Not available Prime Editor') + sys.exit() + + + return model_dir, model_type \ No newline at end of file diff --git a/genet_models/utils/__init__.py b/genet_models/utils/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..f0374409d3019d9464d4b3e83495ff09b8a2ba3e --- /dev/null +++ b/genet_models/utils/__init__.py @@ -0,0 +1,3 @@ +version_ = '1.0.0' + +__version__ = version_ \ No newline at end of file diff --git a/setup.py b/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..59a566db5b2b9505e0ada52b296fd8b83b791f3e --- /dev/null +++ b/setup.py @@ -0,0 +1,34 @@ +import setuptools +import genet_models +from glob import glob + +with open('README.md', 'r', encoding='utf-8') as fh: + long_description = fh.read() + +VERSION = genet_models.__version__ + +setuptools.setup( + name = "genet_models", + version = VERSION, + author = "Goosang Yu", + author_email = "gsyu93@gmail.com", + description = "Models for prediction modules in GenET", + url = "https://github.com/Goosang-Yu/genet-models.git", + packages = setuptools.find_packages(exclude = ['dev_ing', 'dev_ing.*']), + + python_requires = ">=3.7", + classifiers=[ + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "License :: OSI Approved :: MIT License", + "Operating System :: MacOS :: MacOS X", + "Operating System :: POSIX" + ], + + long_description = long_description, + long_description_content_type = "text/markdown", + project_urls={"Bug Tracker": "https://github.com/Goosang-Yu/genet/issues"}, + + include_package_data=True, +) \ No newline at end of file diff --git a/test.ipynb b/test.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..b79225274699cb21cc423731475bce276817d351 --- /dev/null +++ b/test.ipynb @@ -0,0 +1,104 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from genet_models import load_genet_model" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "get model: PE2max - HEK293T\n" + ] + } + ], + "source": [ + "model_dir, model_type = load_genet_model('PE2max', 'HEK293T')" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'e:\\\\github_project\\\\genet-models\\\\genet_models\\\\DeepPrime'" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model_dir" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'DeepPrime/DP_variant_293T_PE2max_Opti_220428'" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model_type" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3.9.13 ('base')", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.13" + }, + "orig_nbformat": 4, + "vscode": { + "interpreter": { + "hash": "456429a4186cf596b072ad5ec1b53207b3d8c219143cb76d95880537d31a740b" + } + } + }, + "nbformat": 4, + "nbformat_minor": 2 +}