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marouenbgmarouenbg
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update test suite (#140) (#141)
-update test suite
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‎.github/workflows/main.yml

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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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#
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# See https://github.com/r-lib/actions/tree/master/examples#readme for
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# additional example workflows available for the R community.
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name: netZooM
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env:
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ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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on:
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push:
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branches:
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- master
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- devel
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pull_request:
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branches:
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- master
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- devel
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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steps:
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- uses: actions/checkout@v2
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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- name: Set up MATLAB
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uses: matlab-actions/setup-matlab@v1
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- name: install bedtools ubuntu
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if: matrix.os == 'ubuntu-latest'
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run: |
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wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz
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tar -zxvf bedtools-2.29.0.tar.gz
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cd bedtools2
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make
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ls
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pwd
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cd ..
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- name: install bedtools macos
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if: matrix.os == 'macos-latest'
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run: |
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wget https://github.com/marouenbg/bedtools2/archive/refs/heads/master.zip
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unzip master.zip
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mv bedtools2-master bedtools2
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cd bedtools2
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make
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ls
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pwd
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cd ..
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- name: Run tests and generate artifacts
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run: |
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ls && pwd
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cd ..
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git clone https://github.com/MOxUnit/MOxUnit.git # Install MOxUnit, which adds itself to the startup path
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git clone https://github.com/MOcov/MOcov.git
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pwd
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ls
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shell: bash
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- name: run actual tests
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run: |
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matlab -batch 'cd ../MOcov;addpath(genpath(pwd));cd ../netZooM;addpath(genpath("/home/runner/work/netZooM/"));back=cd("../MOxUnit/MOxUnit/"); moxunit_set_path(); cd(back); pwd; ls; moxunit_runtests tests -recursive -verbose -junit_xml_file testresults.xml -with_coverage -cover netZooM -cover_exclude tests -cover_xml_file coverage.xml -cover_json_file coveralls.json); exit(double(~ans))'
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- name: report coverage
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run: |
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bash <(curl -s https://codecov.io/bash)
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‎.travis.yml

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This file was deleted.

‎README.md

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[![TRAVIS](https://img.shields.io/travis/netZoo/netZooM/master?label=master)](https://travis-ci.org/netZoo/netZooM/)
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[![TRAVIS](https://img.shields.io/travis/netZoo/netZooM/devel?label=devel)](https://travis-ci.org/netZoo/netZooM/)
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[![netZooM](https://github.com/netZoo/netZooM/actions/workflows/main.yml/badge.svg?branch=master)](https://github.com/netZoo/netZooM/actions/workflows/main.yml)
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[![netZooM](https://github.com/netZoo/netZooM/actions/workflows/main.yml/badge.svg?branch=devel)](https://github.com/netZoo/netZooM/actions/workflows/main.yml)
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[![codecov](https://codecov.io/gh/netZoo/netZooM/branch/devel/graph/badge.svg)](https://codecov.io/gh/netZoo/netZooM)
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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
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[![Documentation Status](https://readthedocs.org/projects/netzoom/badge/?version=latest)](https://netzoom.readthedocs.io/en/latest/?badge=latest)
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[![tutorials](https://img.shields.io/badge/netZooM-tutorials-9cf)](https://github.com/netZoo/netZooM/tree/master/tutorials)
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netZooM is tested on: (OS: Linux + Macos) X (Language: Octave)
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netZooM is tested on: (OS: Ubuntu) X (Language: MATLAB)
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## Description
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netZooM is a MATLAB package of network methods.

‎netZooM/spider/spider_run.m

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DefineRegulatoryRegions(annofile, ranges, regfile, chrinfo);
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end
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CreateEpigeneticMotif(epifile, motifdir, motifhitfile, bedtoolspath,nTF);
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CreateEpigeneticMotif(epifile, motifdir, motifhitfile, bedtoolspath, nTF);
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%%%% Run SPIDER %%%%
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% Build SPIDER prior
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[PriorNet, TFNames, GeneNames]=BuildSPIDERprior(motifhitfile, regfile, bedtoolspath);
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%temporary reduction in number of genes for TRAVIS
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numGenes = 100
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GeneNames = GeneNames(1:numGenes);
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PriorNet = PriorNet(:,1:numGenes);
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% Remove this section for including all genes.
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% Run message-passing
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SpiderNet=SPIDER(PriorNet, eye(length(GeneNames)), eye(length(TFNames)), alpha, computing);

‎netZooM/tools/processData.m

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j = j(indCommPPI);
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weightPPI = weightPPI(indCommPPI);
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TFCoop(sub2ind([NumTFs, NumTFs], i, j)) = weightPPI;
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TFCoop(sub2ind([NumTFs, NumTFs], j, i)) = weightPPI;
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end
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function [GeneMotif,GeneNamesExp,TfMotif,TFNamesInit,NumConditions,...
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ExpInit,TF,gene,weightMotif,weightPPI,TF1,TF2,SampleNames]=...
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readData(exp_file,motif_file,ppi_file)
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% Description:
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% readData reads the input files for PANDA.
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% Inputs:
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% exp_file : file for gene expression
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% motif_file: file for motif data
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% ppi_file : file for TF PPI data
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% Ouputs:
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% GeneMotif : Gene names from gene motif data
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% GeneNamesExp : Gene names from gene expression data
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% TfMotif : TF names from gene motif data
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% TFNamesInit : TF names from gene PPI data
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% NumConditions: Number of gene expression data
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% ExpInit : Gene expression matrix
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% TF : list of TF edges in motif (source)
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% gene : list of gene edges in motif (target)
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% weightMotif : edge weight in the motif network
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% weightPPI : edge weight in the PPI network
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% TF1 : list of TF edges in PPI (source)
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% TF2 : list of TF edges in PPI (target)
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% SampleNames : gene expression samples IDs
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% Author:
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% Marouen Ben Guebila 12/2019
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% Read expression
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disp('Reading in expression data!');
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tic
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exp_file_tbl = readtable(exp_file,'FileType','text','PreserveVariableNames',1);
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SampleNames = exp_file_tbl.Properties.VariableNames;
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ExpInit = exp_file_tbl{:,2:end};
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GeneNamesExp = exp_file_tbl{:,1};
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[NumGenes, NumConditions] = size(ExpInit);
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fprintf('%d genes and %d conditions!\n', NumGenes, NumConditions);
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toc
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if length(unique(GeneNamesExp)) ~= length(GeneNamesExp)
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error('There are duplicate genes in the expression matrix.')
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end
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% Read motif
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disp('Reading in motif data!');
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motif_file_id = fopen(motif_file);
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C = textscan(motif_file_id, '%s%s%f');
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fclose(motif_file_id);
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TF=C{1,1};gene=C{1,2};weightMotif=C{1,3};
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TfMotif = unique(TF);
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GeneMotif= unique(gene);
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% Read PPI
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disp('Reading in ppi data!');
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if(~isempty(ppi_file))
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ppi_file_id = fopen(ppi_file);
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C = textscan(ppi_file_id, '%s%s%f');
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fclose(motif_file_id);
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TF1=C{1,1};TF2=C{1,2};weightPPI=C{1,3};
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end
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TFNamesInit=unique(TF1);
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if ~isequal(TFNamesInit,unique(TF2))
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error('PPI data has missing information.')
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end
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TFCoop(sub2ind([NumTFs, NumTFs], j, i)) = weightPPI;
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end

‎netZooM/tools/readData.m

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function [GeneMotif,GeneNamesExp,TfMotif,TFNamesInit,NumConditions,ExpInit,TF,gene,weightMotif,weightPPI,TF1,TF2,SampleNames]=readData(exp_file,motif_file,ppi_file)
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% Description:
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% readData reads the input files for PANDA.
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% Inputs:
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% exp_file : file for gene expression
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% motif_file: file for motif data
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% ppi_file : file for TF PPI data
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% Ouputs:
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% GeneMotif : Gene names from gene motif data
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% GeneNamesExp : Gene names from gene expression data
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% TfMotif : TF names from gene motif data
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% TFNamesInit : TF names from gene PPI data
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% NumConditions: Number of gene expression data
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% ExpInit : Gene expression matrix
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% TF : list of TF edges in motif (source)
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% gene : list of gene edges in motif (target)
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% weightMotif : edge weight in the motif network
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% weightPPI : edge weight in the PPI network
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% TF1 : list of TF edges in PPI (source)
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% TF2 : list of TF edges in PPI (target)
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% SampleNames : gene expression samples IDs
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% Author:
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% Marouen Ben Guebila 12/2019
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% Read expression
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disp('Reading in expression data!');
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tic
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exp_file_tbl = readtable(exp_file,'FileType','text','PreserveVariableNames',1);
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SampleNames = exp_file_tbl.Properties.VariableNames;
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ExpInit = exp_file_tbl{:,2:end};
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GeneNamesExp = exp_file_tbl{:,1};
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[NumGenes, NumConditions] = size(ExpInit);
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fprintf('%d genes and %d conditions!\n', NumGenes, NumConditions);
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toc
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if length(unique(GeneNamesExp)) ~= length(GeneNamesExp)
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error('There are duplicate genes in the expression matrix.')
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end
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% Read motif
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disp('Reading in motif data!');
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motif_file_id = fopen(motif_file);
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C = textscan(motif_file_id, '%s%s%f');
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fclose(motif_file_id);
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TF=C{1,1};gene=C{1,2};weightMotif=C{1,3};
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TfMotif = unique(TF);
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GeneMotif= unique(gene);
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% Read PPI
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disp('Reading in ppi data!');
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if(~isempty(ppi_file))
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ppi_file_id = fopen(ppi_file);
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C = textscan(ppi_file_id, '%s%s%f');
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fclose(motif_file_id);
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TF1=C{1,1};TF2=C{1,2};weightPPI=C{1,3};
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end
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TFNamesInit=unique(TF1);
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if ~isequal(TFNamesInit,unique(TF2))
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error('PPI data has missing information.')
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end
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end

‎tests/panda2.test.mat

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