Skip to content

Commit

Permalink
refactor: run MAFFT and CD-HIT via WSL on Windows
Browse files Browse the repository at this point in the history
  • Loading branch information
@edkerk
edkerk committed Jan 6, 2022
1 parent 2ab6124 commit f74cb0d
Showing 1 changed file with 90 additions and 64 deletions.
154 changes: 90 additions & 64 deletions external/kegg/getKEGGModelForOrganism.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -598,6 +598,22 @@
%files for more accurate progress reporting
fastaFiles=listFiles(fullfile(dataDir,'fasta','*.fa'));
%Align all sequences using MAFFT
tmpFile=tempname;
%On Windows, paths need to be translated to Unix before parsing it to WSL
if ispc
[~,wslPath.tmpFile]=system(['wsl wslpath ''' tmpFile '''']);
wslPath.tmpFile=wslPath.tmpFile(1:end-1);
%mafft has problems writing to terminal (/dev/stderr) when running
%on WSL via MATLAB, instead write and read progress file
mafftOutput = tempname;
[~,wslPath.mafftOutput]=system(['wsl wslpath ''' mafftOutput '''']);
wslPath.mafftOutput=wslPath.mafftOutput(1:end-1);
[~,wslPath.mafft]=system(['wsl wslpath ''' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '''']);
wslPath.mafft=wslPath.mafft(1:end-1);
[~,wslPath.cdhit]=system(['wsl wslpath ''' fullfile(ravenPath,'software','cd-hit','cd-hit') '''']);
wslPath.cdhit=wslPath.cdhit(1:end-1);
end

for i=1:numel(missingAligned)
%This is checked here because it could be that it is created by a
%parallel process. The faw-files are saved as temporary files to
Expand Down Expand Up @@ -662,78 +678,85 @@
%Do the clustering and alignment if there are more than one
%sequences, otherwise just save the sequence (or an empty file)
if numel(fastaStruct)>1
if seqIdentity==0.9
cdhitInp100=tempname;
fastawrite(cdhitInp100,fastaStruct);
cdhitInp90=tempname;
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
if status~=0
EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
dispEM(EM);
end
%Remove the old tempfile
if exist(cdhitInp100, 'file')
delete([cdhitInp100 '*']);
end
tmpFile=tempname;
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' tmpFile '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
if status~=0
EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
dispEM(EM);
end
%Remove the old tempfile
if exist(cdhitInp90, 'file')
delete([cdhitInp90 '*']);
end
elseif seqIdentity==0.5
cdhitInp100=tempname;
fastawrite(cdhitInp100,fastaStruct);
cdhitInp90=tempname;
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
if status~=0
EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
dispEM(EM);
end
%Remove the old tempfile
if exist(cdhitInp100, 'file')
delete([cdhitInp100 '*']);
end
cdhitInp50=tempname;
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' cdhitInp50 '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
if status~=0
EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
dispEM(EM);
end
%Remove the old tempfile
if exist(cdhitInp90, 'file')
delete([cdhitInp90 '*']);
end
tmpFile=tempname;
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp50 '" -o "' tmpFile '" -c 0.5 -n 3 -M 2000 -aL 0.8']);
if status~=0
EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
dispEM(EM);
end
%Remove the old tempfile
if exist(cdhitInp50, 'file')
delete([cdhitInp50 '*']);
end
elseif seqIdentity~=-1
% if seqIdentity==0.9
% cdhitInp100=tempname;
% fastawrite(cdhitInp100,fastaStruct);
% cdhitInp90=tempname;
% [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
% if status~=0
% EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
% dispEM(EM);
% end
% %Remove the old tempfile
% if exist(cdhitInp100, 'file')
% delete([cdhitInp100 '*']);
% end
% tmpFile=tempname;
% [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' tmpFile '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
% if status~=0
% EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
% dispEM(EM);
% end
% %Remove the old tempfile
% if exist(cdhitInp90, 'file')
% delete([cdhitInp90 '*']);
% end
% elseif seqIdentity==0.5
% cdhitInp100=tempname;
% fastawrite(cdhitInp100,fastaStruct);
% cdhitInp90=tempname;
% [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
% if status~=0
% EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
% dispEM(EM);
% end
% %Remove the old tempfile
% if exist(cdhitInp100, 'file')
% delete([cdhitInp100 '*']);
% end
% cdhitInp50=tempname;
% [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' cdhitInp50 '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
% if status~=0
% EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
% dispEM(EM);
% end
% %Remove the old tempfile
% if exist(cdhitInp90, 'file')
% delete([cdhitInp90 '*']);
% end
% tmpFile=tempname;
% [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp50 '" -o "' tmpFile '" -c 0.5 -n 3 -M 2000 -aL 0.8']);
% if status~=0
% EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
% dispEM(EM);
% end
% %Remove the old tempfile
% if exist(cdhitInp50, 'file')
% delete([cdhitInp50 '*']);
% end
% elseif seqIdentity~=-1
if seqIdentity~=-1
cdhitInpCustom=tempname;
fastawrite(cdhitInpCustom,fastaStruct);
tmpFile=tempname;
if seqIdentity<=1 && seqIdentity>0.7
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 5 -M 2000']);
nparam='5';
elseif seqIdentity>0.6
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 4 -M 2000']);
nparam='4';
elseif seqidentity>0.5
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 3 -M 2000']);
nparam='3';
elseif seqidentity>0.4
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 2 -M 2000']);
nparam='2';
else
EM='The provided seqIdentity must be between 0 and 1\n';
dispEM(EM);
end
if ispc
[~,wslPath.cdhitInpCustom]=system(['wsl wslpath ''' cdhitInpCustom '''']);
wslPath.cdhitInpCustom=wslPath.cdhitInpCustom(1:end-1);
[status, output]=system(['wsl "' wslPath.cdhit '" -T "' num2str(cores) '" -i "' wslPath.cdhitInpCustom '" -o "' wslPath.tmpFile '" -c "' num2str(seqIdentity) '" -n ' nparam ' -M 2000']);
elseif ismac || isunix
[status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n ' nparam ' -M 2000']);
end
if status~=0
EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
dispEM(EM);
Expand All @@ -745,7 +768,6 @@
else
%This means that CD-HIT should be skipped since
%seqIdentity is equal to -1
tmpFile=tempname;
fastawrite(tmpFile,fastaStruct);
end
%Do the alignment for this file
Expand All @@ -754,7 +776,11 @@
elseif isunix
[status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']);
elseif ispc
[status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-win','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']);
[~,wslPath.fawFile]=system(['wsl wslpath ''' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '''']);
wslPath.fawFile=wslPath.fawFile(1:end-1);
[status, output]=system(['wsl "' wslPath.mafft '" --auto --anysymbol --progress "' wslPath.mafftOutput '" --thread "' num2str(cores) '" --out "' wslPath.fawFile '" "' wslPath.tmpFile '"']);
output=fileread(mafftOutput);
delete(mafftOutput);
end
if status~=0
%It could be that alignment failed because only one
Expand Down

0 comments on commit f74cb0d

Please sign in to comment.