diff options
Diffstat (limited to 'src/matlab/multifasta2otutable_rdp7.m')
| -rw-r--r-- | src/matlab/multifasta2otutable_rdp7.m | 212 |
1 files changed, 212 insertions, 0 deletions
diff --git a/src/matlab/multifasta2otutable_rdp7.m b/src/matlab/multifasta2otutable_rdp7.m new file mode 100644 index 0000000..9c83ea9 --- /dev/null +++ b/src/matlab/multifasta2otutable_rdp7.m @@ -0,0 +1,212 @@ +% Quikr multifasta->otu_table_(for_qiime_use) wrapper code written by Gail Rosen -- 2/1/2013
+%This is an example of how to run Quikr on the default RDP_7 training set
+
+%make sure Matlab/Octave is in your path
+%cd /path/to/Quikr
+
+%User-defined variables
+input_directory='../../separated_samples'; %path to input directory of samples
+output_directory='quikr_results'; %path to where want output files to go
+otu_table_name='rdp_otu_table.txt'; %name of output otu_table filename
+%Do not have to define trainingdatabase file here
+[headers,~]=fastaread('../../../data/trainset7_112011.fa'); %read in the training database
+
+mkdir([output_directory])
+thedirs=dir([input_directory]);
+thetime=zeros(numel(thedirs)-1,1);
+names={};
+
+
+if(exist('OCTAVE_VERSION')) %check to see if running Octave or Matlab
+
+%This is Octave Version
+
+
+species=struct();
+keys={};
+
+tic()
+
+i=0;
+%for numdirs=3:5
+for numdirs=3:numel(thedirs)
+i=i+1;
+disp([num2str(i) ' out of ' num2str(numel(thedirs)-2)])
+fastafilename=[input_directory '/' thedirs(numdirs).name];
+[loadfasta,~]=fastaread(fastafilename);
+numreads=numel(loadfasta);
+xstar=quikr(fastafilename); %this will give the predicted reconstruction frequencies
+
+nonzeroentries=find(xstar); %get the indicies of the sequences quikr predicts are in your sample
+proportionscell=num2cell(xstar(nonzeroentries)); %convert the concentrations into a cell array
+namescell=headers(nonzeroentries); %Get the names of the sequences
+namesandproportions={namescell{:}; proportionscell{:}}; %This cell array contains the (unsorted) names of the reconstructed sequences and their concentrations (in the first and second columns respectively)
+
+[a cols]=size(namesandproportions);
+amount=zeros(cols,1);
+for j=1:cols
+ names{j}=namesandproportions{1,j}(1:strfind(namesandproportions{1,j},' ')-1);
+ names{j}=strrep(names{j},'|','_');
+ amount(j)=namesandproportions{2,j};
+if strcmp(keys,names{j})
+ temp=species.(names{j});
+ temp(i)=round(amount(j).*numreads);
+ species.(names{j})=temp;
+ else
+ temp=zeros(numel(thedirs)-3+1,1);
+ temp(i)=round(amount(j).*numreads);
+ if temp(i)==0
+ % do not make a key -- has insignificant counts
+ else
+ species.(names{j})=temp;
+ keys{end+1}=names{j};
+ end
+ end
+end
+
+thefa=strfind(thedirs(numdirs).name,'.fa');
+
+if ~isempty(thedirs(numdirs).name(1:thefa-1))
+ sampleid{i}=thedirs(numdirs).name(1:thefa-1);
+else
+ sampleid{i}='empty_sampleid';
+end
+thetime(i+1)=toc();
+thetime(i+1)
+
+end
+
+disp('Total time to compute Quikr:')
+toc()
+disp('Quikr Average time per file:')
+mean(diff(thetime(1:i+1)))
+
+tic();
+numits=i;
+
+
+fid=fopen([output_directory '/' otu_table_name],'w');
+fprintf(fid,'# QIIME vGail OTU table\n');
+fprintf(fid,'#OTU_ID\t');
+for i=1:numits
+if i<numits
+fprintf(fid,'%s\t',sampleid{i});
+else
+fprintf(fid,'%s',sampleid{i});
+end
+end
+fprintf(fid,'\n');
+
+for k=1:numel(keys)
+truncname=strrep(keys{k},'_','|');
+ fprintf(fid,'%s',truncname);
+
+ temp(:,k)=species.(keys{k});
+ for i=1:numits
+ fprintf(fid,'\t%d',temp(i,k));
+ end
+fprintf(fid,'\n');
+end
+fclose(fid);
+
+disp('Time to output OTU Table:')
+toc()
+
+else
+
+%This is the Matlab version
+
+
+species=containers.Map;
+
+tic()
+
+i=0;
+%for numdirs=3:6
+for numdirs=3:numel(thedirs)
+i=i+1;
+[num2str(i) ' out of ' num2str(numel(thedirs)-2)]
+fastafilename=[input_directory '/' thedirs(numdirs).name];
+[loadfasta,~]=fastaread(fastafilename);
+numreads=numel(loadfasta);
+xstar=quikr(fastafilename); %this will give the predicted reconstruction frequencies
+
+nonzeroentries=find(xstar); %get the indicies of the sequences quikr predicts are in your sample
+proportionscell=num2cell(xstar(nonzeroentries)); %convert the concentrations into a cell array
+namescell=headers(nonzeroentries); %Get the names of the sequences
+namesandproportions={namescell{:}; proportionscell{:}}; %This cell array contains the (unsorted) names of the reconstructed sequences and their concentrations (in the first and second columns respectively)
+
+[a cols]=size(namesandproportions);
+amount=zeros(cols,1);
+for j=1:cols
+ names{j}=namesandproportions{1,j};
+ amount(j)=namesandproportions{2,j};
+ if isKey(species,names{j})
+ temp=species(names{j});
+ temp(i)=round(amount(j).*numreads);
+ species(names{j})=temp;
+ else
+ temp=zeros(numel(thedirs)-3+1,1);
+ temp(i)=round(amount(j).*numreads);
+ if temp(i)==0
+ % insignificant counts -- do not put
+ else
+ species(names{j})=temp;
+ end
+ end
+end
+
+thefa=strfind(thedirs(numdirs).name,'.fa');
+
+if ~isempty(thedirs(numdirs).name(1:thefa-1))
+ sampleid{i}=thedirs(numdirs).name(1:thefa-1);
+else
+ sampleid{i}='empty_sampleid';
+end
+thetime(i+1)=toc();
+thetime(i+1)
+
+end
+
+'Total time to compute Quikr:'
+toc()
+'Quikr Average time per file:'
+mean(diff(thetime(1:i+1)))
+
+tic
+numits=i;
+
+
+fid=fopen([output_directory '/' otu_table_name],'w');
+fprintf(fid,'# QIIME vGail OTU table\n');
+fprintf(fid,'#OTU_ID\t');
+for i=1:numits
+if i<numits
+fprintf(fid,'%s\t',sampleid{i});
+else
+fprintf(fid,'%s',sampleid{i});
+end
+end
+fprintf(fid,'\n');
+
+thekeys=species.keys;
+for k=1:species.Count
+if k==1
+ space=thekeys{k}(20);
+end
+delimit =strfind(thekeys{k},space);
+truncname=thekeys{k}(1:delimit-1);
+ fprintf(fid,'%s',truncname);
+
+ temp(:,k)=species(thekeys{k});
+ for i=1:numits
+ fprintf(fid,'\t%d',temp(i,k));
+ end
+fprintf(fid,'\n');
+end
+fclose(fid);
+
+'Time to output OTU Table:'
+toc
+
+end
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