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Commit 1fe671a6 authored by Vincent Danjean's avatar Vincent Danjean
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correction de bug de la localisation du fait de la modif 9 fichiers 

git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@204 cf695345-040a-0410-a956-b889e835fe2e
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ALTree/Nanova.pm
+ 2
− 2
View file @ 1fe671a6
...@@ -70,13 +70,13 @@ sub FillTableaux ...@@ -70,13 +70,13 @@ sub FillTableaux
my $nb_term = shift; my $nb_term = shift;
if ($present_node->NbChildren()==0) { if ($present_node->NbChildren()==0) {
$presentNode->GetQuantiList(); $present_node->GetQuantiList();
push @{$values}, @{$present_node->GetQuantiList()}; push @{$values}, @{$present_node->GetQuantiList()};
push @{$groups}, $present_node->NbQuanti(); push @{$groups}, $present_node->NbQuanti();
$nb_term++; $nb_term++;
} else { } else {
for my $child ($present_node->GetChildrenList()) { for my $child ($present_node->GetChildrenList()) {
FillTableaux($child, $value, $groups, $nb_term); FillTableaux($child, $values, $groups, $nb_term);
} }
} }
......
altree
+ 70
− 61
View file @ 1fe671a6
...@@ -1039,7 +1039,7 @@ sub SwitchRoot { ...@@ -1039,7 +1039,7 @@ sub SwitchRoot {
} }
################################################################ ################################################################
###################### ASSOCIATION TEST ######################## #################### TRAITE PLS FICHIERS #######################
################################################################ ################################################################
sub TraiteSeveralFiles sub TraiteSeveralFiles
...@@ -1058,7 +1058,7 @@ sub TraiteSeveralFiles ...@@ -1058,7 +1058,7 @@ sub TraiteSeveralFiles
$pmin_min = $res_files->[$i]->{"pmin"}; $pmin_min = $res_files->[$i]->{"pmin"};
} }
} }
print "La pmin minimale est $pmin_min\n"; print "La pmin minimale est $pmin_min, la taille de la distrib pmin est ", scalar(@distrib), "\n";
# sort {$a <=> $b} @distrib; # trie du plus petit au plus grand # sort {$a <=> $b} @distrib; # trie du plus petit au plus grand
my $compte=0; my $compte=0;
...@@ -1516,16 +1516,18 @@ sub main ...@@ -1516,16 +1516,18 @@ sub main
my $racine=$tree->GetRoot(); my $racine=$tree->GetRoot();
my @children=$racine->GetChildrenList(); my @children=$racine->GetChildrenList();
{
my $mat; # EN DEVELOPPEMENT: NANOVA
print "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"; # {
$mat=ALTree::Nanova::Tree2mat($tree->GetRoot()); # my $mat;
ALTree::Nanova::WriteMat($mat); # print "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n";
my $values = []; # $mat=ALTree::Nanova::Tree2mat($tree->GetRoot());
my $groups = []; # ALTree::Nanova::WriteMat($mat);
my $nb_term=0; # my $values = [];
FillTableaux($tree->GetRoot(), $values, $groups, $nb_term); # my $groups = [];
} # my $nb_term=0;
# FillTableaux($tree->GetRoot(), $values, $groups, $nb_term);
# }
$option_require->("permutations", $option_require->("permutations",
"The number of permutations used to calculate". "The number of permutations used to calculate".
...@@ -1596,65 +1598,72 @@ sub main ...@@ -1596,65 +1598,72 @@ sub main
} }
} }
} }
} print "tab_trees @trees\n";
if ($nb_files>1) {
my $p_finale = TraiteSeveralFiles(\@res_files, $nb_files);
print "\n############################################\n";
print "p_value for the $nb_files files = $p_finale\n";
}
########################################################### ###########################################################
# Let's go. Et pour la localisation # Let's go. Et pour la localisation
########################################################### ###########################################################
if ($s_loc==1) { print "tabtrees @trees\n";
#$option_require->("splitmode"); if ($s_loc==1) {
#my($splitmode)=$option_value->("splitmode"); #$option_require->("splitmode");
print "Localisation method using S-character\n"; #my($splitmode)=$option_value->("splitmode");
$option_require->("s-site-number"); print "Localisation method using S-character\n";
my($s_site_nb)=$option_value->("s-site-number"); $option_require->("s-site-number");
$option_require->("s-site-characters"); my($s_site_nb)=$option_value->("s-site-number");
my($s_char_state)=$option_value->("s-site-characters"); $option_require->("s-site-characters");
$option_require->("co-evo"); my($s_char_state)=$option_value->("s-site-characters");
my($co_evo_type)=$option_value->("co-evo"); $option_require->("co-evo");
my($co_evo_type)=$option_value->("co-evo");
# print "co_evo_type=$co_evo_type\n"; # print "co_evo_type=$co_evo_type\n";
#DEBUG print "s_char_state=$s_char_state\n";
if (not ($s_char_state =~
m/([A-Za-z0-9]+)\s*[-=_]*[>]\s*([A-Za-z0-9]+)/)) {
erreur("Invalid character change for character".
" S. It should be Anc -> Der\n", 0);
}
my($s_anc)=$1;
my($s_der)=$2;
my($s_state)= ALTree::Sens->New($s_anc." --> ".$s_der);
my($foret)=ALTree::Foret->New();
#$Data::Dumper::Indent = 0;
for my $file_tree (@trees) {
my $tree=$file_tree->{"tree"};
my ($b_t)=$tree->GetNbBrNonNulle();
my $site=$tree->GetSite($s_site_nb); #DEBUG print "s_char_state=$s_char_state\n";
if (not defined($site)) { if (not ($s_char_state =~
erreur("Invalid value ($s_site_nb) for". m/([A-Za-z0-9]+)\s*[-=_]*[>]\s*([A-Za-z0-9]+)/)) {
" --s-site-number\n", 0); erreur("Invalid character change for character".
" S. It should be Anc -> Der\n", 0);
} }
my($s_anc)=$1;
my($s_der)=$2;
my($s_state)= ALTree::Sens->New($s_anc." --> ".$s_der);
my($foret)=ALTree::Foret->New();
my($s_t, $s_t_rev)=CalculateRit($tree, $s_site_nb, $s_state, #$Data::Dumper::Indent = 0;
$co_evo_type); for my $file_tree (@trees) {
CalculateEit($tree, $s_site_nb, $s_t, $s_t_rev, $b_t); my $tree=$file_tree->{"tree"};
$foret->AddTree($tree);
my ($b_t)=$tree->GetNbBrNonNulle();
my $site=$tree->GetSite($s_site_nb);
if (not defined($site)) {
erreur("Invalid value ($s_site_nb) for".
" --s-site-number\n", 0);
}
print "TREE1, $tree\n";
my($s_t, $s_t_rev)=CalculateRit($tree, $s_site_nb, $s_state,
$co_evo_type);
print "TREE2, $tree\n";
CalculateEit($tree, $s_site_nb, $s_t, $s_t_rev, $b_t);
print "TREE3, $tree\n";
$foret->AddTree($tree);
print "TREE4, $tree\n";
}
$foret->CalculVi();
#PrintAllVi($foret, $s_site_nb);# Non tri
#PrintViMax($foret, $s_site_nb); # Affiche la liste en choisissant
#pour chaque sit, juste le meilleur sens
print "\n";
print "Results:\n";
PrintViMaxSens($foret, $s_site_nb);
} }
$foret->CalculVi(); }
#PrintAllVi($foret, $s_site_nb);# Non tri if ($nb_files>1) {
#PrintViMax($foret, $s_site_nb); # Affiche la liste en choisissant my $p_finale = TraiteSeveralFiles(\@res_files, $nb_files);
#pour chaque sit, juste le meilleur sens print "\n############################################\n";
print "\n"; print "p_value for the $nb_files files = $p_finale\n";
print "Results:\n";
PrintViMaxSens($foret, $s_site_nb);
} }
} }
} }
......
altree-add-S
+ 6
− 5
View file @ 1fe671a6
...@@ -41,9 +41,9 @@ sub ReadCorrespond ...@@ -41,9 +41,9 @@ sub ReadCorrespond
if ($ligne =~ /^$/) { if ($ligne =~ /^$/) {
next; next;
} }
###### Qualitative data ###### ####### Qualitative data ######
if ($data_qual eq "qualitative") { if ($data_qual eq "quali") {
@tableau=split(/\s+/, $ligne); @tableau=split(/\s+/, $ligne);
if ($#tableau != 2) { if ($#tableau != 2) {
die "error in $name_correspond: not 3 columns at line '$ligne'\n"; die "error in $name_correspond: not 3 columns at line '$ligne'\n";
...@@ -54,7 +54,8 @@ sub ReadCorrespond ...@@ -54,7 +54,8 @@ sub ReadCorrespond
die "You have probably exchanged the order of cases and controls in file $name_correspond. It should be: haplo_name m_case_number c_control_number\n"; die "You have probably exchanged the order of cases and controls in file $name_correspond. It should be: haplo_name m_case_number c_control_number\n";
} }
$correspondance{$tableau[0]}->{"case"}=$tableau[1]+0; $correspondance{$tableau[0]}->{"case"}=$tableau[1]+0;
$correspondance{$tableau[0]}->{"control"}=$tableau[2]+0; $correspondance{$tableau[0]}->{"control"}=$tableau[2]+0;
} }
} else { } else {
##### Quantitative data ####### ##### Quantitative data #######
...@@ -244,7 +245,7 @@ sub travail ...@@ -244,7 +245,7 @@ sub travail
# print "$nom\n"; # print "$nom\n";
###### QUALITATIVE ###### ###### QUALITATIVE ######
if ($data_qual eq "qualitative") { if ($data_qual eq "quali") {
if (not exists ($correspondance->{$nom})){ if (not exists ($correspondance->{$nom})){
print STDERR "$nom is not found in the file $name_correspond. Assuming it is the outgroup.\nThe number of cases and controls affected to this sequence is set to 0\n"; print STDERR "$nom is not found in the file $name_correspond. Assuming it is the outgroup.\nThe number of cases and controls affected to this sequence is set to 0\n";
$correspondance->{$nom}->{"case"}=0; $correspondance->{$nom}->{"case"}=0;
......
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