Fixed basic parsing of FASTA files (#25)
This commit is contained in:
Waldir Leoncio
parent
a88f31b3a5
commit
76828387a3
8 changed files with 80 additions and 78 deletions
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@ -87,7 +87,7 @@ for run = 1:nruns
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apu = rows(i);
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PARTITION(i) = initialPartition(apu(1));
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end
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COUNTS = counts; SUMCOUNTS = sumcounts;
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POP_LOGML = computePopulationLogml(1:npops, adjprior, priorTerm);
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LOGDIFF = repmat(-Inf,ninds,npops);
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@ -98,7 +98,7 @@ for run = 1:nruns
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kokeiltu = zeros(nRoundTypes, 1);
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roundTypes = [1 1]; %Ykkösvaiheen sykli kahteen kertaan.
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ready = 0; vaihe = 1;
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if dispText
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disp(' ');
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disp(['Mixture analysis started with initial ' num2str(npops) ' populations.']);
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@ -106,11 +106,11 @@ for run = 1:nruns
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while ready ~= 1
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muutoksia = 0;
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if dispText
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disp(['Performing steps: ' num2str(roundTypes)]);
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end
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for n = 1:length(roundTypes)
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round = roundTypes(n);
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@ -465,7 +465,7 @@ for run = 1:nruns
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npops = poistaTyhjatPopulaatiot(npops);
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POP_LOGML = computePopulationLogml(1:npops, adjprior, priorTerm);
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if dispText
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if dispText
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disp(['Found partition with ' num2str(npops) ' populations.']);
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disp(['Log(ml) = ' num2str(logml)]);
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disp(' ');
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@ -491,7 +491,7 @@ COUNTS = countsBest;
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SUMCOUNTS = sumCountsBest;
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POP_LOGML = pop_logmlBest;
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LOGDIFF = logdiffbest;
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%--------------------------------------------------------------------------
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function clearGlobalVars
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@ -509,9 +509,9 @@ function Z = linkage(Y, method)
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[k, n] = size(Y);
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m = (1+sqrt(1+8*n))/2;
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if k ~= 1 | m ~= fix(m)
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error('The first input has to match the output of the PDIST function in size.');
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error('The first input has to match the output of the PDIST function in size.');
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end
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if nargin == 1 % set default switch to be 'co'
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if nargin == 1 % set default switch to be 'co'
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method = 'co';
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end
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method = lower(method(1:2)); % simplify the switch string.
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@ -519,19 +519,19 @@ monotonic = 1;
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Z = zeros(m-1,3); % allocate the output matrix.
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N = zeros(1,2*m-1);
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N(1:m) = 1;
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n = m; % since m is changing, we need to save m in n.
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n = m; % since m is changing, we need to save m in n.
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R = 1:n;
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for s = 1:(n-1)
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X = Y;
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[v, k] = min(X);
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i = floor(m+1/2-sqrt(m^2-m+1/4-2*(k-1)));
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j = k - (i-1)*(m-i/2)+i;
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Z(s,:) = [R(i) R(j) v]; % update one more row to the output matrix A
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Z(s,:) = [R(i) R(j) v]; % update one more row to the output matrix A
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I1 = 1:(i-1); I2 = (i+1):(j-1); I3 = (j+1):m; % these are temp variables.
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U = [I1 I2 I3];
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I = [I1.*(m-(I1+1)/2)-m+i i*(m-(i+1)/2)-m+I2 i*(m-(i+1)/2)-m+I3];
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J = [I1.*(m-(I1+1)/2)-m+j I2.*(m-(I2+1)/2)-m+j j*(m-(j+1)/2)-m+I3];
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switch method
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case 'si' %single linkage
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Y(I) = min(Y(I),Y(J));
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@ -548,12 +548,12 @@ for s = 1:(n-1)
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end
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J = [J i*(m-(i+1)/2)-m+j];
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Y(J) = []; % no need for the cluster information about j.
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% update m, N, R
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m = m-1;
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m = m-1;
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N(n+s) = N(R(i)) + N(R(j));
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R(i) = n+s;
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R(j:(n-1))=R((j+1):n);
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R(j:(n-1))=R((j+1):n);
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end
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@ -623,7 +623,7 @@ function [muutokset, diffInCounts] = ...
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%
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% Lisäys 25.9.2007:
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% Otettu käyttöön globaali muuttuja LOGDIFF, johon on tallennettu muutokset
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% logml:ssä siirrettäessä yksilöitä toisiin populaatioihin.
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% logml:ssä siirrettäessä yksilöitä toisiin populaatioihin.
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global COUNTS; global SUMCOUNTS;
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global PARTITION; global POP_LOGML;
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@ -647,7 +647,7 @@ COUNTS(:,:,i1) = COUNTS(:,:,i1)+diffInCounts;
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SUMCOUNTS(i1,:) = SUMCOUNTS(i1,:)+diffInSumCounts;
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i2 = find(muutokset==-Inf); % Etsitään populaatiot jotka muuttuneet viime kerran jälkeen.
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i2 = setdiff(i2,i1);
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i2 = setdiff(i2,i1);
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i2_logml = POP_LOGML(i2);
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ni2 = length(i2);
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@ -668,19 +668,19 @@ LOGDIFF(ind,:) = muutokset;
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function diffInCounts = computeDiffInCounts(rows, max_noalle, nloci, data)
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% Muodostaa max_noalle*nloci taulukon, jossa on niiden alleelien
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% lukumäärät (vastaavasti kuin COUNTS:issa), jotka ovat data:n
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% lukumäärät (vastaavasti kuin COUNTS:issa), jotka ovat data:n
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% riveillä rows. rows pitää olla vaakavektori.
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diffInCounts = zeros(max_noalle, nloci);
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for i=rows
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row = data(i,:);
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notEmpty = find(row>=0);
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if length(notEmpty)>0
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diffInCounts(row(notEmpty) + (notEmpty-1)*max_noalle) = ...
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diffInCounts(row(notEmpty) + (notEmpty-1)*max_noalle) + 1;
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end
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end
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end
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%------------------------------------------------------------------------
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@ -693,8 +693,8 @@ function updateGlobalVariables(ind, i2, diffInCounts, ...
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% Suorittaa globaalien muuttujien muutokset, kun yksilö ind
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% on siirretään koriin i2.
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global PARTITION;
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global COUNTS;
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global PARTITION;
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global COUNTS;
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global SUMCOUNTS;
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global POP_LOGML;
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global LOGDIFF;
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@ -724,7 +724,7 @@ function [muutokset, diffInCounts] = laskeMuutokset2( ...
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i1, globalRows, data, adjprior, priorTerm);
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% Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mikä olisi
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% muutos logml:ssä, mikäli korin i1 kaikki yksilöt siirretään
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% koriin i.
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% koriin i.
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global COUNTS; global SUMCOUNTS;
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global PARTITION; global POP_LOGML;
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@ -839,7 +839,7 @@ for pop2 = 1:npops2
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i2 = [1:i1-1 , i1+1:npops];
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i2_logml = POP_LOGML(i2)';
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COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 npops-1]);
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SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[npops-1 1]);
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new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm)';
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@ -848,7 +848,7 @@ for pop2 = 1:npops2
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muutokset(pop2,i2) = new_i1_logml - i1_logml ...
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+ new_i2_logml - i2_logml;
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end
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end
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end
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%------------------------------------------------------------------------------------
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@ -858,7 +858,7 @@ function muutokset = laskeMuutokset5(inds, globalRows, data, adjprior, ...
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% Palauttaa length(inds)*1 taulun, jossa i:s alkio kertoo, mikä olisi
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% muutos logml:ssä, mikäli yksilö i vaihtaisi koria i1:n ja i2:n välillä.
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global COUNTS; global SUMCOUNTS;
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global PARTITION; global POP_LOGML;
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@ -885,14 +885,14 @@ for i = 1:ninds
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SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)-diffInSumCounts;
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COUNTS(:,:,pop2) = COUNTS(:,:,pop2)+diffInCounts;
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SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)+diffInSumCounts;
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new_logmls = computePopulationLogml([i1 i2], adjprior, priorTerm);
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muutokset(i) = sum(new_logmls);
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COUNTS(:,:,pop1) = COUNTS(:,:,pop1)+diffInCounts;
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SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)+diffInSumCounts;
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COUNTS(:,:,pop2) = COUNTS(:,:,pop2)-diffInCounts;
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SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)-diffInSumCounts;
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SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)-diffInSumCounts;
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end
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muutokset = muutokset - i1_logml - i2_logml;
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@ -952,7 +952,7 @@ dist2 = dist(apu);
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function npops = poistaTyhjatPopulaatiot(npops)
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% Poistaa tyhjentyneet populaatiot COUNTS:ista ja
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% Poistaa tyhjentyneet populaatiot COUNTS:ista ja
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% SUMCOUNTS:ista. Päivittää npops:in ja PARTITION:in.
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global COUNTS;
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@ -1006,7 +1006,7 @@ if abs(logml)<10000
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end
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if logml<0
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mjono(pointer-1) = '-';
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end
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end
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else
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suurinYks = 4;
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while abs(logml)/(10^(suurinYks+1)) >= 1
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@ -1035,8 +1035,8 @@ end
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function digit = palautaYks(num,yks)
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% palauttaa luvun num 10^yks termin kertoimen
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% string:inä
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% yks täytyy olla kokonaisluku, joka on
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% string:inä
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% yks täytyy olla kokonaisluku, joka on
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% vähintään -1:n suuruinen. Pienemmillä
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% luvuilla tapahtuu jokin pyöristysvirhe.
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@ -1063,7 +1063,7 @@ if abs(div)<100
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if arvo>0
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mjono(1) = num2str(arvo);
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end
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else
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suurinYks = floor(log10(div));
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mjono(6) = num2str(suurinYks);
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@ -1125,7 +1125,7 @@ T = zeros(m,1);
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end
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end
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end
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function T = clusternum(X, T, k, c)
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m = size(X,1)+1;
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while(~isempty(k))
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@ -1136,7 +1136,7 @@ while(~isempty(k))
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% Assign this node number to leaf children
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t = (children<=m);
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T(children(t)) = c;
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% Move to next level
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k = children(~t) - m;
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end
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