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gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
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Fixed regix bug #67

Closed atuldeshpande closed 2 years ago

atuldeshpande commented 2 years ago

Closes #9

Fixes the bug where regix was ignored after the previous changes to parseParams.m

agitter commented 2 years ago

I tried regenerating the reference output files on a Linux server with MATLAB R2018a. There was error when running SINGE from MATLAB on the new regix data data1/X_regix_test.mat

SINGE_version =

    '0.5.0'

Error using save
Variable 'branches' not found.

Error in parseParams (line 80)
    save(['TempMat' '_' num2str(params.ID)
    '.mat'],'X','ptime','branches','regix','-v7.3');

Error in SINGE_GLG_Test (line 9)
params = parseParams(Data,varargin{:})

Error in SINGE (line 20)
        SINGE_GLG_Test(Data,'--outdir',outdir,args{:})

Error in SINGE_regix (line 16)
SINGE(data,gene_list,outdir,hyperparameter_file);

Loading that .mat file shows where the problem is

>> branches
Undefined function or variable 'branches'.
>> exist('branches')
ans =
     7

The docs indicate 7 means the input is a folder. Do we need to confirm that this function returns 1 instead of using the logical tests?

agitter commented 2 years ago

The error above was fixed in f9ab60a. It may have only occured because I ran SINGE from the MATLAB interactive prompt with a script modeled after SINGE_Example. The addpath call may have added ./.git/branches to the path.

The tests were failing because the adjacency matrices generated with GitHub Actions did not match the reference matrices generated with macOS. I updated the reference adjacency matrices using MATLAB R2018a on Linux. The gene and edge scores did not change in this run.

The tests now pass.