Mercurial > repos > jcb-mpl > eics_check_references
changeset 0:c64a3a2a255a draft
Uploaded
| author | jcb-mpl |
|---|---|
| date | Tue, 27 Apr 2021 14:40:48 +0000 |
| parents | |
| children | 679024760b59 |
| files | 2018_07_check_reference_mz.xml src/mz_0_publi_features4_galaxy.sci src/mz_6bis_durbin_watson.sci test-data/._ref_mz.tab test-data/EICs-merged.tab test-data/ref_mz.tab |
| diffstat | 6 files changed, 410 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/2018_07_check_reference_mz.xml Tue Apr 27 14:40:48 2021 +0000 @@ -0,0 +1,154 @@ +<tool id="2021_05_check_ref_mz" name="EICs -> checks reference mz" version="0.0.1"> + + <description> for 5 determined thresholds for m/z </description> + + <requirements> + <requirement type="package">scilab</requirement> + </requirements> + + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + + <command> <![CDATA[ + if [ -d $__root_dir__/packages/scilab-6.1.0 ]; then $__root_dir__/packages/scilab-6.1.0/bin/scilab-cli -nb -quit -f $* < ${script_file}; else scilab-cli -nb -quit -f $* < ${script_file}; fi + ]]> + </command> + + + <configfiles> + <configfile name="script_file"> <![CDATA[ exec("$__tool_directory__/src/mz_0_publi_features4_galaxy.sci",-1); ... + exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ... + lasterror(); ... + ... + x_in=glx_tab2div("${xtrmz4}"); ... // 20avril21 + [x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}",x_in, ${electron}); ... + ... //[x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}", "${xtrmz4}", ${electron}); ... + ... + div2tab(x_bilan, "${xbilan}"); ... + save("${xsynthese}","x_synthese"); ... + save("${x_tr_mz_trouves}","x_tr_mz4"); ... + if ~isempty(lasterror(%f)); ... + write(0,lasterror()); ... + end; ]]> + </configfile> + </configfiles> + + + <inputs> + <param name="mzref" format="tabular" type="data" label="Reference m/z values" /> + <param name="xtrmz4" format="tabular" type="data" label="EICs-mean" /> + <param name="electron" size="5" value="0" type="integer" label="Electron mass" help="1=correction of the reference m/z values; 0=no correction" /> + </inputs> + + + <outputs> + <data name="xbilan" format="tabular" label="m/z check-summary" /> + <data name="xsynthese" format="mat" label="m/z check-details" /> + <data name="x_tr_mz_trouves" format="mat" label="m/z check-matrix" /> + </outputs> + + + <tests> + + <test> + <param name="mzref" value="ref_mz.tab"/> + <param name="xtrmz4" value="EICs-merged.tab"/> + <output name="xbilan"> + <assert_contents> + <has_text text="0.00034"/> + <has_text text="0.352"/> + </assert_contents> + </output> + </test> + + </tests> +<help> + + +**Author** Jean-Claude Boulet (INRA). + + +--------------------------------------------------- + +======================================================================= +CHECK REFERENCE MZ VALUES AMONG THE EICS-MEAN YIELDED BY THE PROCESSING +======================================================================= + +----------- +Description +----------- + +A matrix of EICs has been yielded by the function: MS-centroid -> EICs-individual or by the function: several EICs-shared -> one EICs-mean. + +The m/z values of these EICs are compared to reference m/z values for 5 pre-determined threshold values for m/z: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100. + +This function is focused on the m/z values, it does not take into account the retention times. + + + +------ +Inputs +------ + +**reference m/z values** + +A tabular file, to the div format (first columns and rows = labels): + +- the first column corresponds to names of chemical compounds; + +- the second column contains the exact (reference) m/z values. + + +**EICs-mean or individual** + +A tabular matrix of (RT x m/z); lines are retention times and columns are EICs. + + +---------- +Parameters +---------- + +**correction of the electron mass** + +A correction can be applied to the reference m/z values. + +- 0: no correction; + +- 1: correction = subtraction of 0.00055 in the positive mode. + + + +------ +Output +------ + +**summary** + +The main results + + +**details** + +A .mat file + + +**extracted EICs** + +An EIC is associated to a reference m/z value if the absolute difference of (EIC minus reference) is under a threshold. + +Five threshold values have been pre-determined: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100 + +This output contains a list of 5 data, each containing the EICs identified as reference m/z values according to a threshold. + +</help> + + +<citations> + +</citations> + + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/mz_0_publi_features4_galaxy.sci Tue Apr 27 14:40:48 2021 +0000 @@ -0,0 +1,205 @@ +function [x_bilan,x_synthese,x_tr_mz_trouves]=mz_0_publi_features4_galaxy(mz_ref,x_tr_mz4,electron,threshold) + + // entrées: ------- + // mz_ref: un fichier tabulation avec 1° colonne = identifiants, 2° colonne = valeurs de m/z; 1° ligne = ids des colonnes + // ce fichier contient les valeurs de référence + // x_tr_mz: un fichier Scilab contenant une matrice d'EICs nommée x_tr_mz4 + // electron: enlever l'électron (1) ou pas (0) + + // sorties: ------- + // x_bilan: les résultats principaux avec en colonne les pas choisis (0,0005, 0,0010 etc) + // et en ligne les indices: recovery / unicity / rmsep / dw + // x_synthese.x_trouves: une liste de divs; pour chacun: .i = indice trouvé; .v = m/z exp. / m/z ref. / Durbin-Watson + // x_synthese.x_reference: un div contenant les références trouvées dans le fichier mz_ref + // x_tr_mz_trouve: la liste de matrices de x_tr_mz4 après extraction des m/z de référence trouvés + // x_bilan: + + + if argn(2)<4 | threshold<0 then + threshold=[0.0005,0.0010,0.0030,0.0050,0.0100]; + end + +// 22avril21 + // charger le fichier des EICs obtenu par Galaxy +// load(x_tr_mz); // la variable s'appelle: x_tr_mz4 + + // 24nov19 +// list_var=who_user(%f); +// list_var=list_var(1); +// for i=1:size(list_var,1); +// execstr(msprintf("xtemp= %s ;",list_var(i))); +// if type(xtemp)==16 then +// x_tr_mz4=xtemp; +// //disp(sel_var,'sel_var=') +// end +// end + +// // patch pour corriger le mauvais fonctionnement du code ci-dessus +// if isdef('x_tr_mz3') then +// x_tr_mz4=x_tr_mz3; +// end + + // si un M devant les valeurs de m/z: le supprimer + //n_v=size(x_tr_mz4.v(i),1); + //for i=1:n_v; + x_tr_mz4.v=strsubst(x_tr_mz4.v,'M',''); + //end + + // obtenir les valeurs de m/z + x_mz=strtod(x_tr_mz4.v); + + + // charger les donnees de reference en csv classique + x_anna0=glx_tab2div(mz_ref); + + //30juin20 on ne garde que 1° colonne + x_anna0=x_anna0(:,1); + + // correction de la masse de l’electron + // 1 -> on corrige; 0 -> on ne corrige pas + x_anna0.d=x_anna0.d-electron*0.00055; + + // arrondis et suppression des valeurs en double + x_anna0.d=0.0001*round(10000*x_anna0.d); // arrondis à E-4 (au lieu de 10E-5 avant le mai18 car ca faisait des doubles) + x_anna0.d=gsort(x_anna0.d,'g','i'); // tri par ordre croissant + [temp,indice_unique]=unique(x_anna0.d); // valeurs uniques a 10E-4 pres + x_anna=x_anna0; + x_anna=x_anna(indice_unique,:); // on garde la precision a 10E-5 + //disp(size(x_anna.d),'size(x_anna.d)=') + + // recherche des composés d'anna: + n_anna=size(x_anna.d,1); + x_verif.d=[x_anna.d zeros(n_anna,1)]; + x_verif.i=x_anna.i; + x_verif.v=[x_anna.v;'nbr of peacks identified']; + x_verif=div(x_verif); + + // gestion de la dimension de threshold + n_thresh=max(size(threshold)); + + // initialisation + recovery=zeros(1,n_thresh); + unicity=zeros(1,n_thresh); + rmsep=zeros(1,n_thresh); + dw=zeros(1,n_thresh); + xtrouves_all=[]; + xtrouves_all2=list(); + + + for k=1:n_thresh; // pour chacune des valeurs de thresh + //disp(k,'k=') + x_trouves=[]; + xtrouves_all=[]; + + for i=1:n_anna; + temp_diff=abs(x_mz-x_anna.d(i)); + trouve=find(temp_diff<threshold(k) & temp_diff==min(temp_diff)); + trouve2=find(temp_diff<threshold(k)); + n_trouve2=max(size(trouve2)); + if trouve==[] then + x_verif.d(i,2)=0; + elseif max(size(trouve))==1 then + x_rajoute=[x_mz(trouve) x_anna.d(i) n_trouve2]; + // dans l'ordre: mz calculee la plus proche de mz anna / mz Anna / nbre de mz plus proches de mz Anna que threshold + if x_trouves==[] then + x_trouves=x_rajoute; + else + x_trouves=[x_trouves;x_rajoute]; + end + end + + // construction de xtrouves_all qui rassemble tous les resultats trouves + if trouve2 ~=[] then + for j=1:n_trouve2; + x_add=[x_mz(trouve2(j)) x_anna.d(i) ]; + if xtrouves_all==[] then + xtrouves_all=x_add; + xtrouves_indices=trouve2(j); + else + xtrouves_all=[xtrouves_all;x_add]; + xtrouves_indices=[xtrouves_indices;trouve2(j)]; + end + end + end + + + end + + if isdef('xtrouves_indices') then // cas ou on a trouve qq chose 13sept18 + + // calcul du rmsep + diff2=x_trouves(:,1)-x_trouves(:,2); + recovery(k)=size(x_trouves,1); + rmsep(k)=sqrt((diff2'*diff2)/recovery(k)); + unicity(k)=sum(x_trouves(:,3))/recovery(k); + if unicity(k)==0 then + pause + end + + // calcul de Durbin-Watson: + //pause + x_dw=x_tr_mz4(:,xtrouves_indices); + res_dw=mz_6bis_durbin_watson(x_dw); + dw(k)=mean(res_dw) /unicity(k); +//pause + res_dw=ones(size(xtrouves_all,1),1); + // rajout de DW a x_trouves_all + xtrouves_all2_temp.d=[xtrouves_all res_dw]; + xtrouves_all2_temp.i=string(xtrouves_indices); + xtrouves_all2_temp.v=['m/z exp.';'m/z ref.';'Durbin-Watson']; + xtrouves_all2_temp=div(xtrouves_all2_temp); + + xtrouves_all2(k)=xtrouves_all2_temp; + + else + xtrouves_all2(k)=[]; + recovery(k)=-1; + unicity(k)=-1; + rmsep(k)=-1; + dw(k)=-1; + + end + + end + + x_bilan.d=[recovery;unicity;rmsep;dw]; + x_bilan.i=['recovery';'unicity';'rmsep';'dw']; + if size(threshold,2)==1 then + threshold=threshold'; + end + x_bilan.v='thresh_'+string(threshold); + + x_bilan=div(x_bilan); + + + + // 27juin: recalcul de unicity pour corriger un bug + n_xtrouves_all2=size(xtrouves_all2); + + nbr_trouves=zeros(1,n_xtrouves_all2); + + for i=1:n_xtrouves_all2; + if xtrouves_all2(i)~=[] then + nbr_trouves(i)=max(size(xtrouves_all2(i).d)); + else + nbr_trouves(i)=1; // 1 car on divise par -1 qq lignes + bas -> on obtient -1 au final + end + end + + + // sorties + x_bilan.d(2,:)=nbr_trouves ./ x_bilan.d(1,:); + + x_synthese.x_trouves=xtrouves_all2; + x_synthese.x_reference=x_anna; + + + // matrice triee ne comprenant que les EICs trouvees + x_tr_mz_trouves=list(); + + for i=1:n_thresh; + x_tr_mz_trouves(i)=x_tr_mz4(:,strtod(x_synthese.x_trouves(i).i)); + end + + +endfunction
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/mz_6bis_durbin_watson.sci Tue Apr 27 14:40:48 2021 +0000 @@ -0,0 +1,21 @@ +function x_dw=mz_6bis_durbin_watson(x_tr_mz) + + // pas de calcul matriciel car pas assez de memoire + // x_dw doit varier entre 0 et 2 + // 0=ce qu on recherche + + [n,q]=size(x_tr_mz.d); + + // calcul de la norme des differences et des vect-colonne de x_tr_mz + x_diff=x_tr_mz.d(2:n,:)-x_tr_mz.d(1:n-1,:); + rmsce=zeros(q,1); + rmsce2=zeros(q,1); + for i=1:q; + rmsce(i)=sqrt((x_diff(:,i)'*x_diff(:,i))/(n-1)); + rmsce2(i)=sqrt((x_tr_mz.d(:,i)'*x_tr_mz.d(:,i))/(n)); + end + + x_dw=rmsce./rmsce2; + + +endfunction
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