refactor: mafftTests and cdhitTests use WSL on PC

kdeperi · Jan 12, 2022 · 24c3021 · 24c3021
1 parent 3524d52
commit 24c3021
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Showing 2 changed files with 22 additions and 2 deletions.
diff --git a/testing/unit_tests/cdhitTests.m b/testing/unit_tests/cdhitTests.m
@@ -47,9 +47,21 @@ function testCdhit(testCase)
 sourceDir = fileparts(which(mfilename));
 copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
 
+% Define WSL paths
+[~,wslPath.fastaFile]=system(['wsl wslpath ''' tmpDIR filesep 'yeast_galactosidases.fa''']);
+wslPath.fastaFile=wslPath.fastaFile(1:end-1);
+[~,wslPath.outFile]=system(['wsl wslpath ''' outFile '''']);
+wslPath.outFile=wslPath.outFile(1:end-1);
+[~,wslPath.cdhit]=system(['wsl wslpath ''' fullfile(ravenPath,'software','cd-hit','cd-hit') '''']);
+wslPath.cdhit=wslPath.cdhit(1:end-1);
+
 %%
 %Run protein clustering with CD-HIT
-[~, ~]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" -o "' outFile '" -c 1.0 -n 5 -M 2000']);
+if ispc
+    [~, ~]=system(['wsl "' wslPath.cdhit '" -T "' num2str(cores) '" -i "' wslPath.fastaFile '" -o "' wslPath.outFile '" -c 1.0 -n 5 -M 2000']);
+else
+    [~, ~]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" -o "' outFile '" -c 1.0 -n 5 -M 2000']);
+end
 
 %%
 %Open actual MAFFT results file

diff --git a/testing/unit_tests/mafftTests.m b/testing/unit_tests/mafftTests.m
@@ -33,14 +33,22 @@ function testMafft(testCase)
 sourceDir = fileparts(which(mfilename));
 copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
 
+% Define WSL paths
+[~,wslPath.fastaFile]=system(['wsl wslpath ''' tmpDIR filesep 'yeast_galactosidases.fa''']);
+wslPath.fastaFile=wslPath.fastaFile(1:end-1);
+[~,wslPath.outFile]=system(['wsl wslpath ''' outFile '''']);
+wslPath.outFile=wslPath.outFile(1:end-1);
+[~,wslPath.mafft]=system(['wsl wslpath ''' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '''']);
+wslPath.mafft=wslPath.mafft(1:end-1);
+
 %%
 %Run protein multi-sequence alignment with MAFFT
 if ismac
     [~, ~]=system(['"' fullfile(ravenPath,'software','mafft','mafft-mac','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" > "' outFile '"']);
 elseif isunix
     [~, ~]=system(['"' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" > "' outFile '"']);
 elseif ispc
-    [~, ~]=system(['"' fullfile(ravenPath,'software','mafft','mafft-win','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" > "' outFile '"']);
+    [~, ~]=system(['wsl "' wslPath.mafft '" --auto --anysymbol --quiet --thread "' num2str(cores) '" --out "' wslPath.outFile '" "' wslPath.fastaFile '"']);
 end
 
 %%