cleaned cami repository

CHANGELOG.txt

-Changelog file for Structures extra.
-https://gitlab.rrz.uni-hamburg.de/bay2046/cami/-/blob/main/CHANGELOG.txt
-
-# CAMI 0.0.1-beta3 (February 11, 2022)
-=======================================
-
-# List of exciting new features
-
-+ LIST OF FILES MODIFIED
-  - cami.sh
-    - funtion for the certificate added
-  - CHANGELOG.txt
-
-# CAMI 0.0.1-beta3 (February 10, 2022)
-=======================================
-
-# List of exciting new features
-
-+ LIST OF FILES MODIFIED
-  - cami_env.yaml the following modules were added:
-    - c-ares=1.18.1=h0d85af4_0
-    - cached-property=1.5.2=hd8ed1ab_1
-    - cached_property=1.5.2=pyha770c72_1
-    - h5py=3.6.0=nompi_py37h0ac0de7_100
-    - hdf5=1.12.1=nompi_hd9e8a45_103
-    - krb5=1.19.2=h289aae4_3
-    - libcurl=7.81.0=h97da3c1_0
-    - libedit=3.1.20191231=h0678c8f_2
-    - libev=4.33=haf1e3a3_1
-    - libnghttp2=1.46.0=hfd382f3_0
-    - libssh2=1.10.0=hd3787cc_2
-    - appdirs==1.4.4
-    - beautifulsoup4==4.10.0
-    - bs4==0.0.1
-    - cssselect==1.1.0
-    - fake-useragent==0.1.11
-    - lxml==4.7.1
-    - parse==1.19.0
-    - pyee==8.2.2
-    - pyppeteer==1.0.2
-    - pyquery==1.4.3
-    - requests-html==0.10.0
-    - soupsieve==2.3.1
-    - tqdm==4.62.3
-    - w3lib==1.22.0
-    - websockets==10.1
-  - CHANGELOG.txt
-
-# CAMI 0.0.1-beta3 (February 05, 2022)
-=======================================
-
-# List of exciting new features
-
-+ LIST OF FILES MODIFIED
-  - README.md
-  - CHANGELOG.txt
-
-+ RENAME SYSTEMBIOLOGIE REPOSITORY TO CAMI
- - rename systembiologie repository to cami
-
-+ LIST OF FILES ADDED
-  - LICENSE
-
-+ TODO
- - importlib_metadata
-
-# CAMI 0.0.1-beta3 (February 03, 2022)
-=======================================
-
-# List of exciting new features
-
-+ LIST OF FILES DELETED FOR BEING DUPLICATES
-	- robust_cami/*
-	- tools/robust/cami_option_1.py
-	- tools/robust/cami_option_2.py
-	- tools/robust/robustFUN.py
-	- tools/robust/robustFUN2.py
-
-+ LIST OF FILES MODIFIED
-  - README.md
-  - doc/cami.txt
-
-+ LIST OF FILES ADDED
-  - CHANGELOG.txt
-	- src/
-
-+ TODO
- - rename systembiology repository to cami

LICENSE

-Copyright (c) 2022 Marcos Chow Castro
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

README.md

@@ -16,12 +16,13 @@
 
 Consensus Active Module Identification(CAMI)
 
-CAMI has two functions:
+CAMI's main purposes are:
 - Consensus Prediction: Use different algorithms to find active disease
-  modules in a given PPI-network and combines their results.
-- Uses a protein-protein-interaction-network (PPI-network) and
-   a seed list as input Evaluation:
-   Evaluate different tools with respect to the consensus of multiple tools.
+  modules in a given PPI-network and combine their results with a consensus function
+- Evaluation pipelines: Compare different result sets of algorithms to each other and their consensus using DIGEST and/or a pipeline that estimates the ability to rediscover removed seeds from a given seed set
+
+Input: a protein-protein-interaction-network (PPI-network) and a seed list
+Output: multiple sets of predicted Active moduless
 
 Cami was tested with the `python 3.7` interpreter, we recommend using this
 version of `python` for a better user experience.
@@ -48,13 +49,10 @@ proper installation and use of cami
 2. Update cami:
    sh cami.sh
    option: u    update env cami
-3. Install cami certificate:
-   sh cami.sh
-   option: ce fix drugstone certificates
-4. Execute a example:
+3. Execute a example:
    sh cami.sh
    option: ex   execute a example
-5. Remove tmp file:
+4. Remove tmp file:
    sh cami.sh
    option: cl   remove tmp file
 ```

cami_src/example_run.py

@@ -9,5 +9,5 @@ chdir((sys.argv[0].rsplit('/', 1))[0])
 networkfile = "../data/input/networks/example_network.tsv"
 seedfile = "../data/input/seeds/example_seeds.txt"
 identifier = "example_run"
-command = f'./cami.py -n {networkfile} -s {seedfile} -id {identifier} -img -p --f;'
+command = f'./cami.py -n {networkfile} -s {seedfile} -id {identifier} -p --f;'
 subprocess.call(command, shell=True)
\ No newline at end of file

docker_cami/.dockerignore

-.DS_Store

docker_cami/.env

-# test

module_to_exec.txt

-### START CMDS ### {{{ DONE
-## ADD CHANNELS
-conda config --add channels defaults
-conda config --add channels conda-forge
-conda config --add channels bioconda
-## CREATE
-conda create --name cami python=3.7
-## ACTIVATE
-conda activate cami
-## UPDATE ENVIRONMENT
-conda env update cami --file=cami_env.yaml
-## INSTALL
-conda install numpy matplotlib pandas networkx pip jupyter
-pip install pcst_fast
-
-
-## DELETE ENVIRONMENT
-conda env remove -n cami
-## SHOW ENVIRONMENT LIST
-conda info --envs
-## DEACTIVATE
-conda deactivate
-## EXPORT ENVIRONMENT
-conda env export > cami_env.yaml
-### END CMDS #### }}}
-
-### amim-test-suite ###{{{
-github -> https://github.com/dbblumenthal/amim-test-suite
-## graph-tool
-https://graph-tool.skewed.de
-conda create --name gt -c conda-forge graph-tool
-conda activate gt
-#}}}
-
-### START ROBUST.GIT ### {{{ DONE
-github -> https://github.com/bionetslab/robust.git
-# Install conda environment as follows (there also exists a environment.yml
-# but it contains more packages than necessary)
-conda create --name cami python=3.7
-conda activate cami
-conda install numpy matplotlib pandas networkx pip jupyter
-pip install pcst_fast
-# Eingabe
-python robust.py data/human_annotated_PPIs_brain.txt data/ms_seeds.txt ms.graphml 0.25 0.9 30 0.1
-# The positional arguments are:
-[1] file providing the network in the form of an edgelist
-    (tab-separated table, columns 1 & 2 will be used)
-[2] file with the seed genes (if table contains more than
-    one column they must be tab-separated; the first column
-    will be used only)
-[3] path to output file
-[4] initial fraction
-[5] reduction factor
-[6] number of steiner trees to be computed
-[7] threshold
-# Ausführen
-python robust.py data/human_annotated_PPIs_brain.txt data/ms_seeds.txt ms.graphml 0.25 0.9 30 0.1
-# Ausgabe
--> ms.graphml
-<?xml version='1.0' encoding='utf-8'?>
-<graphml ...>
-</graphml>
-### END ROBUST.GIT #### }}}
-
-### START DIAMOnD ### {{{DONE
-gihub -> https://github.com/dinaghiassian/DIAMOnD
-python3 DIAMOnD.py  network_file seed_file  n  alpha(optional)  outfile_name(optional)
-Directory Example
-contains two input files:
-seed_genes.txt (list of genes associated with a phenotype of interest)
-PPI.txt (Protein-protein interaction network. note that gene IDs should be consistent in the two input files)
-The following command will generate the first 100 DIAMOnD nodes and save them in a file)
-# Eingabe
-usage: python3 DIAMOnD.py network_file seed_file n alpha(optional) outfile_name (optional)
------------------------------------------------------------------
-network_file : The edgelist must be provided as any delimiter-separated
-               table. Make sure the delimiter does not exit in gene IDs
-               and is consistent across the file.
-               The first two columns of the table will be
-               interpreted as an interaction gene1 <==> gene2
-seed_file    : table containing the seed genes (if table contains
-               more than one column they must be tab-separated;
-               the first column will be used only)
-n            : desired number of DIAMOnD genes, 200 is a reasonable
-               starting point.
-alpha        : an integer representing weight of the seeds,default
-               value is set to 1
-outfile_name : results will be saved under this file name
-               by default the outfile_name is set to "first_n_added_nodes_weight_alpha.txt"
-# Ausführen
-python3  DIAMOnD.py  Example/PPI.txt  Example/seed_genes.txt  100
-# Ausgabe
--> first_100_added_nodes_weight_1.txt
-#rank	DIAMOnD_node	p_hyper
-1	4758	3.993956525332022e-07
-### END DIAMOnD ### }}}
-
-### START DOMINO ### {{{DONE
-github -> https://github.com/Shamir-Lab/DOMINO
-## From conda (Bioconda)
-## working on Linux Informatik with Linux 18.04 LTS and conda
-# Make sure the Bioconda repository and its dependencies are available:
-conda config --add channels defaults
-conda config --add channels conda-forge
-conda config --add channels bioconda
-# Create a virtual environment in conda. For example:
-conda create --name domino-env
-conda activate domino-env
-# Then, install domino via pip:
-# conda install domino
-python setup.py install
-# Eingabe
-slicer -n examples/string.sif -o slices_file.txt
-domino --active_genes_files </path/to/dataset1,/path/to/dataset2...> --network_file </path/to/network.sif> --slices_file <slices_file.txt> --output_folder </path/to/output_folder> [-sth <slices_threshold> -mth <putative_modules_threshold>]
-domino -a examples/tnfa_active_genes_file.txt -n examples/huri.sif -s test_domino/slices_file.txt -o test_domino -sth test_domino -mth test_domino
-[-sth <slices_threshold> -mth <putative_modules_threshold>]
-# Ausführen
-# Ausgabe
--> slices_file.txt
-
-### END DOMINO ### }}}
-
-# vim: set ft=text fdm=marker:

tree_cami.txt

-.
-├── bin
-├── cami
-│  ├── AlgorithmWrapper.py
-│  ├── cami.py
-│  ├── cami_suite.py
-│  ├── degradome.py
-│  ├── DiamondWrapper.py
-│  ├── DominoWrapper.py
-│  ├── drugstone.py
-│  ├── example_run.py
-│  ├── HHotNetWrapper.py
-│  ├── ncbi.py
-│  ├── preprocess.py
-│  ├── RobustWrapper.py
-│  └── test_run.py
-├── cami.sh
-├── cami_env.yaml
-├── CHANGELOG.txt
-├── data
-│  ├── input
-│  ├── output
-│  └── tmp
-├── doc
-│  ├── cami.txt
-│  └── tags
-├── docker_cami
-│  ├── docker-compose.yaml
-│  ├── Dockerfile
-│  └── README.md
-├── drugstone_certificates.txt
-├── LICENSE
-├── Makefile
-├── module_to_exec.txt
-├── README.md
-├── src
-├── tools
-│  ├── DIAMOnD
-│  ├── diamond_packages.txt
-│  ├── HHotNet
-│  └── robust
-└── tree_cami.txt