.DS_Store
.gitignore
LICENSE.txt
MANIFEST.in
PKG-INFO
README.rst
setup.cfg
setup.py
.eggs/README.txt
.eggs/nose-1.3.7-py3.6.egg/EGG-INFO/PKG-INFO
.eggs/nose-1.3.7-py3.6.egg/EGG-INFO/SOURCES.txt
.eggs/nose-1.3.7-py3.6.egg/EGG-INFO/dependency_links.txt
.eggs/nose-1.3.7-py3.6.egg/EGG-INFO/entry_points.txt
.eggs/nose-1.3.7-py3.6.egg/EGG-INFO/not-zip-safe
.eggs/nose-1.3.7-py3.6.egg/EGG-INFO/top_level.txt
.eggs/nose-1.3.7-py3.6.egg/man/man1/nosetests.1
.eggs/nose-1.3.7-py3.6.egg/nose/__init__.py
.eggs/nose-1.3.7-py3.6.egg/nose/__main__.py
.eggs/nose-1.3.7-py3.6.egg/nose/case.py
.eggs/nose-1.3.7-py3.6.egg/nose/commands.py
.eggs/nose-1.3.7-py3.6.egg/nose/config.py
.eggs/nose-1.3.7-py3.6.egg/nose/core.py
.eggs/nose-1.3.7-py3.6.egg/nose/exc.py
.eggs/nose-1.3.7-py3.6.egg/nose/failure.py
.eggs/nose-1.3.7-py3.6.egg/nose/importer.py
.eggs/nose-1.3.7-py3.6.egg/nose/inspector.py
.eggs/nose-1.3.7-py3.6.egg/nose/loader.py
.eggs/nose-1.3.7-py3.6.egg/nose/proxy.py
.eggs/nose-1.3.7-py3.6.egg/nose/pyversion.py
.eggs/nose-1.3.7-py3.6.egg/nose/result.py
.eggs/nose-1.3.7-py3.6.egg/nose/selector.py
.eggs/nose-1.3.7-py3.6.egg/nose/suite.py
.eggs/nose-1.3.7-py3.6.egg/nose/twistedtools.py
.eggs/nose-1.3.7-py3.6.egg/nose/usage.txt
.eggs/nose-1.3.7-py3.6.egg/nose/util.py
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/__init__.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/__main__.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/case.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/commands.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/config.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/core.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/exc.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/failure.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/importer.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/inspector.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/loader.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/proxy.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/pyversion.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/result.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/selector.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/suite.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/twistedtools.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/__pycache__/util.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/ext/__init__.py
.eggs/nose-1.3.7-py3.6.egg/nose/ext/dtcompat.py
.eggs/nose-1.3.7-py3.6.egg/nose/ext/__pycache__/__init__.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/ext/__pycache__/dtcompat.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__init__.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/allmodules.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/attrib.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/base.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/builtin.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/capture.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/collect.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/cover.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/debug.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/deprecated.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/doctests.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/errorclass.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/failuredetail.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/isolate.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/logcapture.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/manager.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/multiprocess.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/plugintest.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/prof.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/skip.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/testid.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/xunit.py
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/__init__.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/allmodules.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/attrib.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/base.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/builtin.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/capture.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/collect.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/cover.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/debug.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/deprecated.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/doctests.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/errorclass.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/failuredetail.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/isolate.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/logcapture.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/manager.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/multiprocess.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/plugintest.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/prof.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/skip.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/testid.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/plugins/__pycache__/xunit.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/sphinx/__init__.py
.eggs/nose-1.3.7-py3.6.egg/nose/sphinx/pluginopts.py
.eggs/nose-1.3.7-py3.6.egg/nose/sphinx/__pycache__/__init__.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/sphinx/__pycache__/pluginopts.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/tools/__init__.py
.eggs/nose-1.3.7-py3.6.egg/nose/tools/nontrivial.py
.eggs/nose-1.3.7-py3.6.egg/nose/tools/trivial.py
.eggs/nose-1.3.7-py3.6.egg/nose/tools/__pycache__/__init__.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/tools/__pycache__/nontrivial.cpython-36.pyc
.eggs/nose-1.3.7-py3.6.egg/nose/tools/__pycache__/trivial.cpython-36.pyc
.eggs/nose-1.3.7-py3.7.egg/EGG-INFO/DESCRIPTION.rst
.eggs/nose-1.3.7-py3.7.egg/EGG-INFO/PKG-INFO
.eggs/nose-1.3.7-py3.7.egg/EGG-INFO/RECORD
.eggs/nose-1.3.7-py3.7.egg/EGG-INFO/WHEEL
.eggs/nose-1.3.7-py3.7.egg/EGG-INFO/entry_points.txt
.eggs/nose-1.3.7-py3.7.egg/EGG-INFO/metadata.json
.eggs/nose-1.3.7-py3.7.egg/EGG-INFO/top_level.txt
.eggs/nose-1.3.7-py3.7.egg/man/man1/nosetests.1
.eggs/nose-1.3.7-py3.7.egg/nose/__init__.py
.eggs/nose-1.3.7-py3.7.egg/nose/__main__.py
.eggs/nose-1.3.7-py3.7.egg/nose/case.py
.eggs/nose-1.3.7-py3.7.egg/nose/commands.py
.eggs/nose-1.3.7-py3.7.egg/nose/config.py
.eggs/nose-1.3.7-py3.7.egg/nose/core.py
.eggs/nose-1.3.7-py3.7.egg/nose/exc.py
.eggs/nose-1.3.7-py3.7.egg/nose/failure.py
.eggs/nose-1.3.7-py3.7.egg/nose/importer.py
.eggs/nose-1.3.7-py3.7.egg/nose/inspector.py
.eggs/nose-1.3.7-py3.7.egg/nose/loader.py
.eggs/nose-1.3.7-py3.7.egg/nose/proxy.py
.eggs/nose-1.3.7-py3.7.egg/nose/pyversion.py
.eggs/nose-1.3.7-py3.7.egg/nose/result.py
.eggs/nose-1.3.7-py3.7.egg/nose/selector.py
.eggs/nose-1.3.7-py3.7.egg/nose/suite.py
.eggs/nose-1.3.7-py3.7.egg/nose/twistedtools.py
.eggs/nose-1.3.7-py3.7.egg/nose/usage.txt
.eggs/nose-1.3.7-py3.7.egg/nose/util.py
.eggs/nose-1.3.7-py3.7.egg/nose/ext/__init__.py
.eggs/nose-1.3.7-py3.7.egg/nose/ext/dtcompat.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/__init__.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/allmodules.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/attrib.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/base.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/builtin.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/capture.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/collect.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/cover.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/debug.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/deprecated.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/doctests.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/errorclass.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/failuredetail.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/isolate.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/logcapture.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/manager.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/multiprocess.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/plugintest.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/prof.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/skip.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/testid.py
.eggs/nose-1.3.7-py3.7.egg/nose/plugins/xunit.py
.eggs/nose-1.3.7-py3.7.egg/nose/sphinx/__init__.py
.eggs/nose-1.3.7-py3.7.egg/nose/sphinx/pluginopts.py
.eggs/nose-1.3.7-py3.7.egg/nose/tools/__init__.py
.eggs/nose-1.3.7-py3.7.egg/nose/tools/nontrivial.py
.eggs/nose-1.3.7-py3.7.egg/nose/tools/trivial.py
bin/cpat.py
bin/make_hexamer_tab.py
bin/make_logitModel.py
dat/.Rapp.history
dat/Fly_Hexamer.tsv
dat/Fly_cutoff.txt
dat/Fly_logitModel.RData
dat/Human_Hexamer.tsv
dat/Human_cutoff.txt
dat/Human_logitModel.RData
dat/Mouse_Hexamer.tsv
dat/Mouse_cutoff.txt
dat/Mouse_logitModel.RData
dat/Zebrafish_logitModel.RData
dat/zebrafish_Hexamer.tsv
dat/zebrafish_cutoff.txt
docs_v3/.DS_Store
docs_v3/Makefile
docs_v3/conf.py
docs_v3/index.rst
docs_v3/make.bat
docs_v3/_build/.DS_Store
docs_v3/_build/doctrees/environment.pickle
docs_v3/_build/doctrees/index.doctree
docs_v3/_build/html/.buildinfo
docs_v3/_build/html/genindex.html
docs_v3/_build/html/index.html
docs_v3/_build/html/objects.inv
docs_v3/_build/html/search.html
docs_v3/_build/html/searchindex.js
docs_v3/_build/html/_images/CPAT_performance.png
docs_v3/_build/html/_images/Figure_1A_features_3D.png
docs_v3/_build/html/_images/Figure_4.png
docs_v3/_build/html/_images/Figure_S2.png
docs_v3/_build/html/_images/UQCR10.jpg
docs_v3/_build/html/_images/UQCR10.png
docs_v3/_build/html/_images/cpat.png
docs_v3/_build/html/_sources/index.rst.txt
docs_v3/_build/html/_static/CPAT_comparison.png
docs_v3/_build/html/_static/CPAT_performance.png
docs_v3/_build/html/_static/Figure_1A_features_3D.png
docs_v3/_build/html/_static/Figure_1_4features.png
docs_v3/_build/html/_static/Figure_2A_features_3D.png
docs_v3/_build/html/_static/Figure_2B_10fold_ROC.png
docs_v3/_build/html/_static/Figure_2C_10fold_Recall.png
docs_v3/_build/html/_static/Figure_2D_10fold_cutoff.png
docs_v3/_build/html/_static/Figure_4.png
docs_v3/_build/html/_static/Figure_S2.png
docs_v3/_build/html/_static/Human_10fold_sens_vs_spec.png
docs_v3/_build/html/_static/UQCR10.jpg
docs_v3/_build/html/_static/UQCR10.png
docs_v3/_build/html/_static/basic.css
docs_v3/_build/html/_static/basic_screenshot.png
docs_v3/_build/html/_static/classic.css
docs_v3/_build/html/_static/cpat.png
docs_v3/_build/html/_static/default.css
docs_v3/_build/html/_static/doctools.js
docs_v3/_build/html/_static/documentation_options.js
docs_v3/_build/html/_static/file.png
docs_v3/_build/html/_static/hgt_genome_28e2b_b4e1f0.png
docs_v3/_build/html/_static/jquery-3.2.1.js
docs_v3/_build/html/_static/jquery-3.5.1.js
docs_v3/_build/html/_static/jquery.js
docs_v3/_build/html/_static/language_data.js
docs_v3/_build/html/_static/minus.png
docs_v3/_build/html/_static/plus.png
docs_v3/_build/html/_static/pygments.css
docs_v3/_build/html/_static/searchtools.js
docs_v3/_build/html/_static/sidebar.js
docs_v3/_build/html/_static/underscore-1.3.1.js
docs_v3/_build/html/_static/underscore.js
docs_v3/_static/CPAT_comparison.png
docs_v3/_static/CPAT_performance.png
docs_v3/_static/Figure_1A_features_3D.png
docs_v3/_static/Figure_1_4features.png
docs_v3/_static/Figure_2A_features_3D.png
docs_v3/_static/Figure_2B_10fold_ROC.png
docs_v3/_static/Figure_2C_10fold_Recall.png
docs_v3/_static/Figure_2D_10fold_cutoff.png
docs_v3/_static/Figure_4.png
docs_v3/_static/Figure_S2.png
docs_v3/_static/Human_10fold_sens_vs_spec.png
docs_v3/_static/UQCR10.jpg
docs_v3/_static/UQCR10.png
docs_v3/_static/basic_screenshot.png
docs_v3/_static/cpat.png
docs_v3/_static/hgt_genome_28e2b_b4e1f0.png
lib/.DS_Store
lib/psyco_full.py
lib/CPAT.egg-info/PKG-INFO
lib/CPAT.egg-info/SOURCES.txt
lib/CPAT.egg-info/dependency_links.txt
lib/CPAT.egg-info/not-zip-safe
lib/CPAT.egg-info/requires.txt
lib/CPAT.egg-info/top_level.txt
lib/__pycache__/psyco_full.cpython-37.pyc
lib/cpmodule/FrameKmer.py
lib/cpmodule/__init__.py
lib/cpmodule/fickett.py
lib/cpmodule/find_orfs.py
lib/cpmodule/ireader.py
lib/cpmodule/utils.py
lib/cpmodule/__pycache__/FrameKmer.cpython-37.pyc
lib/cpmodule/__pycache__/FrameKmer.cpython-38.pyc
lib/cpmodule/__pycache__/__init__.cpython-37.pyc
lib/cpmodule/__pycache__/__init__.cpython-38.pyc
lib/cpmodule/__pycache__/fasta.cpython-37.pyc
lib/cpmodule/__pycache__/fickett.cpython-37.pyc
lib/cpmodule/__pycache__/fickett.cpython-38.pyc
lib/cpmodule/__pycache__/find_orfs.cpython-37.pyc
lib/cpmodule/__pycache__/find_orfs.cpython-38.pyc
lib/cpmodule/__pycache__/ireader.cpython-37.pyc
lib/cpmodule/__pycache__/ireader.cpython-38.pyc
lib/cpmodule/__pycache__/utils.cpython-37.pyc
lib/cpmodule/__pycache__/utils.cpython-38.pyc
test/.Rapp.history
test/CPAT_run_info.log
test/Human_Hexamer.tsv
test/Human_coding_transcripts_hg19.bed
test/Human_logitModel.RData
test/Human_noncoding_transcripts_hg19.bed
test/Human_test_coding_mRNA.fa
test/Human_test_coding_mRNA_hg19.bed
test/Human_test_noncoding_RNA.fa.gz
test/Human_test_noncoding_hg19.bed
test/human_train.logit.RData
test/human_train.make_logitModel.r
test/human_train2.feature.xls
test/human_train2.logit.RData
test/human_train2.make_logitModel.r
test/human_train_BED_CDS.xls
test/make_logitModel_run_info.log
test/out6.ORF_prob.best.tsv
test/out6.ORF_prob.tsv
test/out6.ORF_seqs.fa
test/out6.no_ORF.txt
test/out6.r
test/test.sh