Browse Source

changed yml file to generate env, added kmedoids lib, added citations file

nicolas-zimmermann 2 years ago
parent
commit
6f5fa0f130
4 changed files with 122 additions and 14 deletions
  1. 1 0
      doc/citations
  2. 0 14
      src/config_projet.yml
  3. 120 0
      src/environment.yml
  4. 1 0
      src/projet8.py

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doc/citations View File

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+mlpy for use of k-medoid : D. Albanese, R. Visintainer, S. Merler, S. Riccadonna, G. Jurman, C. Furlanello. mlpy: Machine Learning Python, 2012. arXiv:1202.6548 [bib] 

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src/config_projet.yml View File

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-name: projet-court
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-channels:
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-        - defaults
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-        - bioconda
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-        - conda-forge
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-dependencies:
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-        - numpy
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-        - pandas
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-        - scipy
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-        - jupyter
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-        - jupyterlab
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-        - pip
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-        - pip:
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-                - pbxplore

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src/environment.yml View File

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+name: projet-court
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+channels:
3
+  - defaults
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+dependencies:
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+  - _libgcc_mutex=0.1=main
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+  - attrs=19.1.0=py37_1
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+  - backcall=0.1.0=py37_0
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+  - blas=1.0=mkl
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+  - bleach=3.1.0=py37_0
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+  - ca-certificates=2019.5.15=1
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+  - certifi=2019.6.16=py37_1
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+  - dbus=1.13.6=h746ee38_0
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+  - decorator=4.4.0=py37_1
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+  - defusedxml=0.6.0=py_0
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+  - entrypoints=0.3=py37_0
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+  - expat=2.2.6=he6710b0_0
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+  - fontconfig=2.13.0=h9420a91_0
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+  - freetype=2.9.1=h8a8886c_1
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+  - glib=2.56.2=hd408876_0
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+  - gmp=6.1.2=h6c8ec71_1
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+  - gst-plugins-base=1.14.0=hbbd80ab_1
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+  - gstreamer=1.14.0=hb453b48_1
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+  - icu=58.2=h9c2bf20_1
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+  - intel-openmp=2019.4=243
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+  - ipykernel=5.1.2=py37h39e3cac_0
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+  - ipython=7.8.0=py37h39e3cac_0
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+  - ipython_genutils=0.2.0=py37_0
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+  - ipywidgets=7.5.1=py_0
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+  - jedi=0.15.1=py37_0
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+  - jinja2=2.10.1=py37_0
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+  - jpeg=9b=h024ee3a_2
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+  - json5=0.8.5=py_0
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+  - jsonschema=3.0.2=py37_0
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+  - jupyter=1.0.0=py37_7
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+  - jupyter_client=5.3.1=py_0
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+  - jupyter_console=6.0.0=py37_0
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+  - jupyter_core=4.5.0=py_0
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+  - jupyterlab=1.1.3=pyhf63ae98_0
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+  - jupyterlab_server=1.0.0=py_1
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+  - libedit=3.1.20181209=hc058e9b_0
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+  - libffi=3.2.1=hd88cf55_4
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+  - libgcc-ng=9.1.0=hdf63c60_0
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+  - libgfortran-ng=7.3.0=hdf63c60_0
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+  - libpng=1.6.37=hbc83047_0
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+  - libsodium=1.0.16=h1bed415_0
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+  - libstdcxx-ng=9.1.0=hdf63c60_0
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+  - libuuid=1.0.3=h1bed415_2
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+  - libxcb=1.13=h1bed415_1
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+  - libxml2=2.9.9=hea5a465_1
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+  - markupsafe=1.1.1=py37h7b6447c_0
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+  - mistune=0.8.4=py37h7b6447c_0
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+  - mkl=2019.4=243
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+  - mkl-service=2.3.0=py37he904b0f_0
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+  - mkl_fft=1.0.14=py37ha843d7b_0
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+  - mkl_random=1.0.2=py37hd81dba3_0
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+  - nbconvert=5.5.0=py_0
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+  - nbformat=4.4.0=py37_0
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+  - ncurses=6.1=he6710b0_1
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+  - notebook=6.0.1=py37_0
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+  - numpy=1.16.5=py37h7e9f1db_0
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+  - numpy-base=1.16.5=py37hde5b4d6_0
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+  - openssl=1.1.1d=h7b6447c_1
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+  - pandas=0.25.1=py37he6710b0_0
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+  - pandoc=2.2.3.2=0
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+  - pandocfilters=1.4.2=py37_1
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+  - parso=0.5.1=py_0
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+  - pcre=8.43=he6710b0_0
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+  - pexpect=4.7.0=py37_0
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+  - pickleshare=0.7.5=py37_0
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+  - pip=19.2.2=py37_0
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+  - prometheus_client=0.7.1=py_0
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+  - prompt_toolkit=2.0.9=py37_0
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+  - ptyprocess=0.6.0=py37_0
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+  - pygments=2.4.2=py_0
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+  - pyqt=5.9.2=py37h05f1152_2
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+  - pyrsistent=0.14.11=py37h7b6447c_0
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+  - python=3.7.4=h265db76_1
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+  - python-dateutil=2.8.0=py37_0
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+  - pytz=2019.2=py_0
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+  - pyzmq=18.1.0=py37he6710b0_0
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+  - qt=5.9.7=h5867ecd_1
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+  - qtconsole=4.5.5=py_0
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+  - readline=7.0=h7b6447c_5
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+  - scipy=1.3.1=py37h7c811a0_0
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+  - send2trash=1.5.0=py37_0
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+  - setuptools=41.0.1=py37_0
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+  - sip=4.19.8=py37hf484d3e_0
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+  - six=1.12.0=py37_0
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+  - sqlite=3.29.0=h7b6447c_0
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+  - terminado=0.8.2=py37_0
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+  - testpath=0.4.2=py37_0
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+  - tk=8.6.8=hbc83047_0
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+  - tornado=6.0.3=py37h7b6447c_0
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+  - traitlets=4.3.2=py37_0
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+  - wcwidth=0.1.7=py37_0
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+  - webencodings=0.5.1=py37_1
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+  - wheel=0.33.4=py37_0
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+  - widgetsnbextension=3.5.1=py37_0
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+  - xz=5.2.4=h14c3975_4
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+  - zeromq=4.3.1=he6710b0_3
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+  - zlib=1.2.11=h7b6447c_3
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+  - pip:
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+    - biopython==1.74
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+    - cycler==0.10.0
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+    - griddataformats==0.5.0
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+    - gsd==1.8.1
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+    - joblib==0.13.2
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+    - kiwisolver==1.1.0
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+    - matplotlib==3.1.1
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+    - mdanalysis==0.20.1
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+    - mmtf-python==1.1.2
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+    - mock==3.0.5
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+    - msgpack==0.6.1
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+    - networkx==2.3
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+    - pbxplore==1.3.8
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+    - pillow==6.1.0
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+    - pyclustering==0.9.1
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+    - pyparsing==2.4.2
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+prefix: /home/sdv/m2bi/nzimmermann/.conda/envs/projet-court
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+

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src/projet8.py View File

@@ -5,6 +5,7 @@ import numpy as np
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 import pbxplore as pbx
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 import sys
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 from scipy.spatial.distance import squareform, pdist, jaccard 
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+from pyclustering.cluster.kmedoids import kmedoids # for kmedoids method
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 class Conformations:
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     """