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adding in env file and example criteria files for users
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@kristyhoran
kristyhoran committed Oct 4, 2024
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287 changes: 138 additions & 149 deletions environment.yml
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dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- alsa-lib=1.2.6.1=h7f98852_0
- bc=1.07.1=h7f98852_0
- bcftools=1.12=h45bccc9_1
- bedtools=2.30.0=h468198e_3
- boost-cpp=1.74.0=h75c5d50_8
- brotli=1.0.9=h166bdaf_7
- brotli-bin=1.0.9=h166bdaf_7
- brotlipy=0.7.0=py39hb9d737c_1004
- bwa=0.7.17=h7132678_9
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2021.10.8=ha878542_0
- cairo=1.16.0=ha61ee94_1011
- certifi=2021.10.8=py39hf3d152e_2
- cffi=1.15.0=py39h4bc2ebd_0
- charset-normalizer=2.0.12=pyhd8ed1ab_0
- colorama=0.4.4=pyh9f0ad1d_0
- cryptography=36.0.2=py39hd97740a_1
- cssselect2=0.2.1=pyh9f0ad1d_1
- csvtk=0.23.0=h9ee0642_0
- curl=7.83.1=h7bff187_0
- delly=0.8.7=he03298f_1
- expat=2.4.8=h27087fc_0
- alsa-lib=1.2.12=h4ab18f5_0
- bcftools=1.20=h8b25389_1
- boost-cpp=1.85.0=h3c6214e_4
- bwa=0.7.18=he4a0461_1
- bzip2=1.0.8=h4bc722e_7
- c-ares=1.33.1=heb4867d_0
- ca-certificates=2024.8.30=hbcca054_0
- cairo=1.18.0=hebfffa5_3
- csvtk=0.30.0=h9ee0642_2
- delly=1.2.8=hf9970c3_0
- eigen=3.4.0=h00ab1b0_0
- expat=2.6.3=h5888daf_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.14.0=h8e229c2_0
- font-ttf-ubuntu=0.83=h77eed37_2
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.33.3=py39hb9d737c_0
- freebayes=1.3.5=py39hba5d119_3
- freetype=2.10.4=h0708190_1
- fribidi=1.0.10=h36c2ea0_0
- gatk4=4.2.6.1=hdfd78af_0
- gettext=0.19.8.1=h73d1719_1008
- giflib=5.2.1=h36c2ea0_2
- git=2.35.3=pl5321h36853c3_0
- glib=2.70.2=h780b84a_4
- glib-tools=2.70.2=h780b84a_4
- graphite2=1.3.13=h58526e2_1001
- gsl=2.6=he838d99_2
- harfbuzz=4.2.1=hf9f4e7c_0
- html5lib=1.1=pyh9f0ad1d_0
- htslib=1.12=h9093b5e_1
- icu=70.1=h27087fc_0
- idna=3.3=pyhd8ed1ab_0
- jbig=2.1=h7f98852_2003
- jinja2=3.1.2=pyhd8ed1ab_0
- jpeg=9e=h166bdaf_1
- k8=0.2.5=hd03093a_2
- freebayes=1.3.8=h6a68c12_2
- freetype=2.12.1=h267a509_2
- gettext=0.22.5=he02047a_3
- gettext-tools=0.22.5=he02047a_3
- giflib=5.2.2=hd590300_0
- graphite2=1.3.13=h59595ed_1003
- gsl=2.7=he838d99_0
- harfbuzz=9.0.0=hda332d3_1
- htslib=1.21=h5efdd21_0
- icu=75.1=he02047a_0
- jsoncpp=1.9.6=h84d6215_0
- keyutils=1.6.1=h166bdaf_0
- kmc=3.2.1=hf1761c0_2
- krb5=1.19.3=h3790be6_0
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- lerc=2.2.1=h9c3ff4c_0
- libblas=3.9.0=14_linux64_openblas
- libbrotlicommon=1.0.9=h166bdaf_7
- libbrotlidec=1.0.9=h166bdaf_7
- libbrotlienc=1.0.9=h166bdaf_7
- libcblas=3.9.0=14_linux64_openblas
- libcups=2.3.3=hf5a7f15_1
- libcurl=7.83.1=h7bff187_0
- libdeflate=1.7=h7f98852_5
- krb5=1.21.3=h659f571_0
- lcms2=2.16=hb7c19ff_0
- ld_impl_linux-64=2.40=hf3520f5_7
- lerc=4.0.0=h27087fc_0
- libasprintf=0.22.5=he8f35ee_3
- libasprintf-devel=0.22.5=he8f35ee_3
- libblas=3.9.0=24_linux64_openblas
- libboost=1.85.0=h0ccab89_4
- libboost-devel=1.85.0=h00ab1b0_4
- libboost-headers=1.85.0=ha770c72_4
- libcblas=3.9.0=24_linux64_openblas
- libcups=2.3.3=h4637d8d_4
- libcurl=8.10.1=hbbe4b11_0
- libdeflate=1.20=hd590300_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libev=4.33=hd590300_2
- libexpat=2.6.3=h5888daf_0
- libffi=3.4.2=h7f98852_5
- libgcc-ng=12.1.0=h8d9b700_16
- libgfortran-ng=12.1.0=h69a702a_16
- libgfortran5=12.1.0=hdcd56e2_16
- libglib=2.70.2=h174f98d_4
- libgomp=12.1.0=h8d9b700_16
- libiconv=1.16=h516909a_0
- libnghttp2=1.47.0=h727a467_0
- libnsl=2.0.0=h7f98852_0
- libopenblas=0.3.20=pthreads_h78a6416_0
- libpng=1.6.37=h21135ba_2
- libssh2=1.10.0=ha56f1ee_2
- libstdcxx-ng=12.1.0=ha89aaad_16
- libtiff=4.3.0=hf544144_1
- libuuid=2.32.1=h7f98852_1000
- libwebp=1.2.2=h3452ae3_0
- libwebp-base=1.2.2=h7f98852_1
- libxcb=1.13=h7f98852_1004
- libzlib=1.2.11=h166bdaf_1014
- lofreq=2.1.5=py39h2dde2f4_4
- lz4-c=1.9.3=h9c3ff4c_1
- markupsafe=2.1.1=py39hb9d737c_1
- minimap2=2.24=h7132678_1
- munkres=1.1.4=pyh9f0ad1d_0
- ncurses=6.2=h58526e2_4
- openjdk=11.0.9.1=hc6918da_3
- openjpeg=2.4.0=hb52868f_1
- openssl=1.1.1o=h166bdaf_0
- pango=1.50.7=hbd2fdc8_0
- parallel=20220222=ha770c72_0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.37=h032f7d1_0
- perl=5.32.1=2_h7f98852_perl5
- pillow=9.1.0=py39hae2aec6_2
- pilon=1.24=hdfd78af_0
- python=3.9.9=h62f1059_0_cpython
- pip=22.1
- pixman=0.40.0=h36c2ea0_0
- pthread-stubs=0.4=h36c2ea0_1001
- pycparser=2.21=pyhd8ed1ab_0
- pydyf=0.1.2=pyhd8ed1ab_0
- pyopenssl=22.0.0=pyhd8ed1ab_0
- pyphen=0.12.0=pyhd8ed1ab_0
- pysocks=1.7.1=py39hf3d152e_5
- python_abi=3.9=2_cp39
- readline=8.1=h46c0cb4_0
- requests=2.27.1=pyhd8ed1ab_0
- libgcc=14.1.0=h77fa898_1
- libgcc-ng=14.1.0=h69a702a_1
- libgettextpo=0.22.5=he02047a_3
- libgettextpo-devel=0.22.5=he02047a_3
- libgfortran=14.1.0=h69a702a_1
- libgfortran-ng=14.1.0=h69a702a_1
- libgfortran5=14.1.0=hc5f4f2c_1
- libglib=2.80.3=h315aac3_2
- libgomp=14.1.0=h77fa898_1
- libiconv=1.17=hd590300_2
- libidn2=2.3.7=hd590300_0
- libjpeg-turbo=3.0.0=hd590300_1
- libnghttp2=1.58.0=h47da74e_1
- libnsl=2.0.1=hd590300_0
- libopenblas=0.3.27=pthreads_hac2b453_1
- libpng=1.6.44=hadc24fc_0
- libsqlite=3.46.1=hadc24fc_0
- libssh2=1.11.0=h0841786_0
- libstdcxx=14.1.0=hc0a3c3a_1
- libstdcxx-ng=14.1.0=h4852527_1
- libtiff=4.6.0=h1dd3fc0_3
- libunistring=0.9.10=h7f98852_0
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.4.0=hd590300_0
- libxcb=1.16=hb9d3cd8_1
- libxcrypt=4.4.36=hd590300_1
- libzlib=1.3.1=h4ab18f5_1
- ncurses=6.5=he02047a_1
- openjdk=22.0.1=h8651b0f_1
- openssl=3.3.2=hb9d3cd8_0
- parallel=20240722=ha770c72_0
- pcre2=10.44=hba22ea6_2
- perl=5.32.1=7_hd590300_perl5
- pip=24.2=pyh8b19718_1
- pixman=0.43.2=h59595ed_0
- pthread-stubs=0.4=hb9d3cd8_1002
- python=3.10.14=hd12c33a_0_cpython
- readline=8.2=h8228510_1
- samclip=0.4.0=hdfd78af_1
- samtools=1.12=h9aed4be_1
- setuptools=62.2.0=py39hf3d152e_0
- six=1.16.0=pyh6c4a22f_0
- snpeff=5.0=hdfd78af_1
- sqlite=3.37.0=h9cd32fc_0
- tabixpp=1.1.0=he28291e_6
- tinycss2=1.1.1=pyhd8ed1ab_0
- tk=8.6.12=h27826a3_0
- tqdm=4.64.0=pyhd8ed1ab_0
- trimmomatic=0.39=hdfd78af_2
- tzdata=2022a=h191b570_0
- unicodedata2=14.0.0=py39hb9d737c_1
- urllib3=1.26.9=pyhd8ed1ab_0
- vcflib=1.0.2=h3198e80_5
- weasyprint=55.0=pyhd8ed1ab_0
- webencodings=0.5.1=py_1
- wheel=0.37.1=pyhd8ed1ab_0
- xorg-fixesproto=5.0=h7f98852_1002
- xorg-inputproto=2.3.2=h7f98852_1002
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.2=h7f98852_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- samtools=1.20=h50ea8bc_1
- setuptools=73.0.1=pyhd8ed1ab_0
- snpeff=5.2=hdfd78af_1
- tabixpp=1.1.2=h27d5293_3
- tk=8.6.13=noxft_h4845f30_101
- vcflib=1.0.10=hdcf5f25_1
- wfa2-lib=2.3.5=h4ac6f70_2
- wget=1.21.4=hda4d442_0
- wheel=0.44.0=pyhd8ed1ab_0
- xorg-fixesproto=5.0=hb9d3cd8_1003
- xorg-inputproto=2.3.2=hb9d3cd8_1003
- xorg-kbproto=1.0.7=hb9d3cd8_1003
- xorg-libice=1.1.1=hd590300_0
- xorg-libsm=1.2.4=h7391055_0
- xorg-libx11=1.8.9=hb711507_1
- xorg-libxau=1.0.11=hb9d3cd8_1
- xorg-libxdmcp=1.1.3=hb9d3cd8_1
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxfixes=5.0.3=h7f98852_1004
- xorg-libxi=1.7.10=h7f98852_0
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxtst=1.2.3=h7f98852_1002
- xorg-recordproto=1.14.2=h7f98852_1002
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.5=h516909a_1
- zlib=1.2.11=h166bdaf_1014
- zstd=1.5.2=ha95c52a_0
- xorg-libxi=1.7.10=h4bc722e_1
- xorg-libxrender=0.9.11=hd590300_0
- xorg-libxt=1.3.0=hd590300_1
- xorg-libxtst=1.2.5=h4bc722e_0
- xorg-recordproto=1.14.2=hb9d3cd8_1003
- xorg-renderproto=0.11.1=hb9d3cd8_1003
- xorg-xextproto=7.3.0=hb9d3cd8_1004
- xorg-xproto=7.0.31=hb9d3cd8_1008
- xz=5.2.6=h166bdaf_0
- zlib=1.3.1=h4ab18f5_1
- zstd=1.5.6=ha6fb4c9_0
- pip:
- numpy==1.22.3
- pandas==1.4.2
- psutil==5.9.0
- python-dateutil==2.8.2
- pytz==2022.1
- xlsxwriter==3.0.3
prefix: ~/conda/envs/tbtamr
- annotated-types==0.7.0
- certifi==2024.8.30
- charset-normalizer==3.3.2
- exceptiongroup==1.2.2
- idna==3.10
- iniconfig==2.0.0
- joblib==1.4.2
- mutamr==0.0.1
- numpy==2.1.1
- packaging==24.1
- pandas==2.2.2
- pluggy==1.5.0
- psutil==6.0.0
- pydantic==2.9.2
- pydantic-core==2.23.4
- pysam==0.22.1
- pytest==8.3.3
- python-dateutil==2.9.0.post0
- pytz==2024.2
- requests==2.32.3
- six==1.16.0
- tabulate==0.9.0
- tbtamr==1.0.2
- tomli==2.0.1
- tqdm==4.66.5
- typing-extensions==4.12.2
- tzdata==2024.1
- unidecode==1.3.8
- urllib3==2.2.3
prefix: ~/.conda/envs/tbtamr
13 changes: 13 additions & 0 deletions example_criteria/classification_criteria_who_v2.csv
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classification,shape,drug_class_condition,required_condition,comparator,exclusion_comparator,exlusionary_condition,optional_condition
Mono-resistance predicted (Hr-TB),==1,first-line,isoniazid,in,,,
Mono-resistance predicted (RR-TB),==1,first-line,rifampicin,in,,,
Mono-resistance predicted ,==1,first-line,ethambutol,in,,,
Mono-resistance predicted ,==1,first-line,pyrazinamide,in,,,
Poly-resistance predicted (RR-TB),>1,first-line,rifampicin&ethambutol,in,not in,isoniazid,
Poly-resistance predicted (RR-TB),>1,first-line,rifampicin&pyrazinamide,in,not in,isoniazid,
Poly-resistance predicted (Hr-TB),>1,first-line,isoniazid&pyrazinamide,in,not in,rifampicin,
Poly-resistance predicted (Hr-TB),>1,first-line,isoniazid&ethambutol,in,not in,rifampicin,
Poly-resistance predicted,>1,first-line,ethambutol&pyrazinamide,in,not in,rifampicin|isoniazid,
Multi-drug resistance predicted (MDR-TB),>1,first-line,isoniazid&rifampicin,in,,,
Pre-Extensive/Extensive drug-resistance predicted,>1,,rifampicin&moxifloxacin,in,,,isoniazid
Pre-Extensive/Extensive drug-resistance predicted,>1,,rifampicin&levofloxacin,in,,,isoniazid
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