diff --git a/CHANGELOG.txt b/CHANGELOG.txt
deleted file mode 100644
index cfa131a0f3c30d40cd70fb5cfae1c86ca7f216ed..0000000000000000000000000000000000000000
--- a/CHANGELOG.txt
+++ /dev/null
@@ -1,88 +0,0 @@
-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
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index c3da25cd137a6adb2f50df8ad96ce7768a6ad464..0000000000000000000000000000000000000000
--- a/LICENSE
+++ /dev/null
@@ -1,19 +0,0 @@
-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.
diff --git a/README.md b/README.md
index 36244d7781b1907f0a93d8bb09a196e0c24206bc..6064d5e25bab1ae05e237d6619239fedde78ff27 100644
--- a/README.md
+++ b/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
```
diff --git a/cami_src/example_run.py b/cami_src/example_run.py
index ed3ed87b932cd79ed53552806d82fff9a8ba8346..386b499259a88e161573ec44ca59527a847c9b28 100755
--- a/cami_src/example_run.py
+++ b/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
diff --git a/docker_cami/.dockerignore b/docker_cami/.dockerignore
deleted file mode 100644
index e43b0f988953ae3a84b00331d0ccf5f7d51cb3cf..0000000000000000000000000000000000000000
--- a/docker_cami/.dockerignore
+++ /dev/null
@@ -1 +0,0 @@
-.DS_Store
diff --git a/docker_cami/.env b/docker_cami/.env
deleted file mode 100644
index 83c831f0b085c70509b1fbb0a0131a9a32e691ac..0000000000000000000000000000000000000000
--- a/docker_cami/.env
+++ /dev/null
@@ -1 +0,0 @@
-# test
diff --git a/module_to_exec.txt b/module_to_exec.txt
deleted file mode 100644
index 9362899a5550f660f743f8ae572d12ef328c924a..0000000000000000000000000000000000000000
--- a/module_to_exec.txt
+++ /dev/null
@@ -1,123 +0,0 @@
-### 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:
diff --git a/tree_cami.txt b/tree_cami.txt
deleted file mode 100644
index a0ec6efe3c2f5c3620ac51e03a0de4635561476f..0000000000000000000000000000000000000000
--- a/tree_cami.txt
+++ /dev/null
@@ -1,42 +0,0 @@
-.
-├── 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