Added source Matlab code for reference

matlab/linkage/readbaps.m

@@ -0,0 +1,188 @@
+function [data, filename] = readbaps(varargin)
+MAXNAME = 200;
+
+if nargin == 0
+    [filename, pathname] = uigetfile( ...
+        {'*.txt', 'BAPS Sequence Files (*.txt)';
+        '*.*',  'All Files (*.*)'}, ...
+        'Load BAPS sequence data');
+    if ~(filename), data=[]; return; end
+    filename=[pathname,filename];
+end
+
+if nargin == 1 
+    [filename,pathname] = uigetfile( ...
+        {'*.txt', 'BAPS Sequence Files (*.txt)';
+        '*.*',  'All Files (*.*)'}, ...
+        sprintf('Load the BAPS sequence data for gene %s',varargin{1}) );
+    if ~(filename), data = [];
+        return;
+    end
+    filename=[pathname,filename];
+end
+
+if nargin == 2
+    [filename,pathname] = uigetfile( ...
+        {'*.txt', 'BAPS Sequence Files (*.txt)';
+        '*.*',  'All Files (*.*)'}, ...
+        sprintf('Load the BAPS sequence file for gene %s',varargin{1}) );
+    if ~(filename),data = [];
+        return;
+    end
+    filename=[pathname,filename];
+    chosen_index = varargin{2};
+end
+
+if nargin < 3
+    % [seqtype, geneticcode]=selectSeqTypeAndGeneticCode;
+    seqtype = 2;
+    geneticcode = 1;
+    if (isempty(seqtype)|isempty(geneticcode)), data=[]; return; end
+end
+
+
+pause(0.0001);
+if ~ischar(filename)
+    error('BAPS:InvalidInput','Input must be a character array')
+    data = [];
+    return;
+end
+
+if ~(exist(filename,'file') | exist(fullfile(cd,filename),'file')),
+    %  is a valid filename ?
+    error('BAPS:InvalidInput','Input must be a valid file')
+    data = [];
+    return;
+end
+
+file = fopen(filename, 'r');
+display('---------------------------------------------------');
+display(['Reading BAPS sequence data from: ',filename,'...']);
+display('---------------------------------------------------');
+% Now we are looking for the maximum length of the sequence
+n=0;    % the number of sequences
+m=0;    % the maximum length
+cm = 0; % current sequence length
+
+while 1
+    [x,nr] = fscanf(file,'%c',1);
+    if nr == 0 break; end;
+    if x==' '  % new sequence started
+        if cm ~=m & m >0
+            % fprintf(['*** ERROR: Different sequence length found in allelic ','%d','.\n'],n+1);
+            disp('***ERROR: Incorrect BAPS sequence data.');
+            data = [];
+            fclose(file);
+            return;
+        end
+        if cm > m m=cm; end;
+        cm = 0;
+        fgets(file);
+        n=n+1;
+    else
+        if isletter(x) | x=='-' | x == '?'
+            cm=cm+1;
+        end;
+    end;
+end
+
+if cm > m m=cm; end;
+
+% go throught the file
+if  (m==0 | n==0)
+    % display(['*** ERROR: Unmatched data for gene ' varargin{1}]);
+    disp('***ERROR: Incorrect BAPS sequence data.');
+    data = [];
+    fclose(file);
+    return;
+end
+
+Ss = char(m); S = [];
+str = zeros(1,MAXNAME);
+sizes = zeros(1,n);
+frewind(file);
+% names=[];
+names={};
+i=1;j=1;
+id = 0;
+while 1
+    [x,nr] = fscanf(file,'%c',1);
+    if nr == 0 
+        break; 
+    end;
+    if x==' '  % new sequence started
+        if i~= 0 % save the sequence
+            % str=x;
+            [x, sizes(i)]=size(Ss);
+            S=strvcat(S,Ss);
+            Ss = []; Ss = char(m);
+        end;
+        str=fgetl(file); % read the name, we remove the '>' symbol      
+        % names=strvcat(names,str);
+        % pos=find(str==' ');
+        % if ~(isempty(pos))
+        %    str=str(1:pos(1,1));
+        % end
+        names{i}=str2num(str);
+        i=i+1;
+        
+        if nargin == 1
+            if isempty(findstr(str, varargin{1}))
+                display(['*** ERROR: Unmatched data for gene ' varargin{1}]);
+                data = [];
+                fclose(file);
+                return
+            end
+        end
+        % disp(['Processing in: ' str]);
+        id = id + 1;
+        j=1;
+    else
+        if isletter(x) | x== '-' | x=='?'
+            % processing the sequence symbol
+            Ss(j) = upper(x);
+            j=j+1;
+        end;
+    end;
+end
+% S=strvcat(S,Ss);
+[x, sizes(i)]=size(Ss);
+if ~isempty(find(S==' '))
+    disp('***ERROR: unequal sequence length.');
+    data = [];
+    fclose(file);
+    return
+end
+
+if exist('chosen_index','var')
+   S = S(chosen_index,:);
+   names = names(chosen_index);
+end
+aln.seqtype = seqtype;
+aln.geneticcode = geneticcode;
+aln.seqnames = names;
+aln.seq = S;
+aln = encodealn(aln);
+data = aln.seq;
+% if nargin == 1
+%     if isempty(findstr(names{1},varargin{1}))
+%         disp(['*** ERROR: The file does not contain the required gene ' varargin{1}]);
+%         data = [];
+%         return;
+%     end
+% end
+% display(['# of allelic types: ' num2str(size(aln.seq,1))]);
+% display(['# of nucleotides: ' num2str(size(aln.seq,2))]);
+% ----------------------
+% order_index = [1:size(aln.seq,1)]';
+% data = [aln.seq order_index]; % Append the index column in the end.
+% ----------------------
+try,
+data = [data cell2mat(names)'];
+catch,
+    disp('*** ERROR: Failed in loading the BAPS data.');
+    disp('*** ERROR: Inidividual indices are not numerically sequential.');
+    data = [];
+end
+fclose(file);
+