From 113df79ec906d606bccd82da8684d42aee178085 Mon Sep 17 00:00:00 2001
From: Vincent Danjean <Vincent.Danjean@ens-lyon.org>
Date: Thu, 18 May 2006 16:28:34 +0000
Subject: [PATCH] ajout du quantitatif pour phase/paup dans altree-convert
git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@194 cf695345-040a-0410-a956-b889e835fe2e
---
altree-convert | 82 +++++++++++++++++++++++++++++++++++++++-----------
1 file changed, 64 insertions(+), 18 deletions(-)
diff --git a/altree-convert b/altree-convert
index 6ffc693..6e54c88 100755
--- a/altree-convert
+++ b/altree-convert
@@ -8,7 +8,7 @@ use Getopt::Long; # qw(:config permute);
use Pod::Usage;
#use Getopt::Std;
-our($opt_h, $opt_r, $opt_i, $opt_j, $opt_o, $opt_t, $opt_p, $opt_c);
+our($opt_h, $opt_r, $opt_i, $opt_j, $opt_o, $opt_t, $opt_p, $opt_c, $opt_q);
our $VERSION;
$VERSION = sprintf "0.%03d", q$Revision$ =~ /(\d+)/g;
@@ -289,27 +289,43 @@ sub ReadFAMHAP
sub TransfoData
{
my($hash_ind)=shift;
+ my($data_quali)=shift;
my($j)=1;
my($ind, %hash_haplo);
+
foreach $ind (keys %{$hash_ind}) {
- if (($hash_ind->{$ind}->{"statut"} != 0) && ($hash_ind->{$ind}->{"statut"} !=1)) {
- die "Invalid disease statut for individual $ind: ", $hash_ind->{$ind}->{"statut"}, "\n";
+ if ($data_quali eq "quali") {
+ if (($hash_ind->{$ind}->{"statut"} != 0)
+ && ($hash_ind->{$ind}->{"statut"} !=1)) {
+ die "Invalid disease statut for individual $ind: ",
+ $hash_ind->{$ind}->{"statut"}, "\n";
+ } else {
+ my($i);
+ for ($i=1; $i<=2; $i++) {
+ $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[$hash_ind->{$ind}->{"statut"}]++;
+ $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[0]+=0; # moche mais pour eviter les non défini dans affichage
+ $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[1]+=0;
+
+ if (!exists $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[2]) {
+ $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[2]=$j;
+ $j++;
+ }
+ }
+ }
} else {
- my($i);
- for ($i=1; $i<=2; $i++) {
- $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[$hash_ind->{$ind}->{"statut"}]++;
- $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[0]+=0; # moche mais pour eviter les non défini dans affichage
- $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[1]+=0;
-
- if (!exists $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[2]) {
- $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->[2]=$j;
+ # In this case, $hash_haplo is a hash with $haplo as keys and a
+ # ref on a tab containing the quantitative values as values.
+ for (my $i=1; $i<=2; $i++) {
+ push (@{$hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->{"valeurs"}}, $hash_ind->{$ind}->{"statut"});
+ if (!exists $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->{"name"}) {
+ $hash_haplo{$hash_ind->{$ind}->{"haplo".$i}}->{"name"}=$j;
$j++;
}
+
}
}
-
}
my($nb_haplo);
$nb_haplo=keys %hash_haplo;
@@ -337,11 +353,21 @@ sub MakeCorrespondanceFile
{
my($hash_haplo)=shift;
my($file_corres)=shift;
+ my $data_quali = shift;
my($haplo);
open (CORRESP, '>', $file_corres) || die "Unable to open correspond.txt: $!\n";
foreach $haplo (keys %{$hash_haplo}) {
- printf CORRESP "H%.3i\tm%.3i\tc%.3i\n", $hash_haplo->{$haplo}->[2],$hash_haplo->{$haplo}->[1], $hash_haplo->{$haplo}->[0];
+ if ($data_quali eq "quali") {
+ printf CORRESP "H%.3i\tm%.3i\tc%.3i\n", $hash_haplo->{$haplo}->[2],$hash_haplo->{$haplo}->[1], $hash_haplo->{$haplo}->[0];
+ } else {
+ printf CORRESP "H%.3i\t", $hash_haplo->{$haplo}->{"name"};
+ foreach my $valeurs (@{$hash_haplo->{$haplo}->{"valeurs"}}) {
+ print CORRESP "$valeurs\t";
+ }
+ print CORRESP "\n";
+ }
}
+
close(CORRESP);
}
@@ -379,10 +405,11 @@ sub BuildPAUP
my($nb_loci)=shift;
my($data_type)=shift;
my($file_corres)= shift;
+ my $data_quali=shift;
# my($der, $anc);
my($write_data_type);
- MakeCorrespondanceFile($hash_haplo, $file_corres);
+ MakeCorrespondanceFile($hash_haplo, $file_corres, $data_quali);
#($anc, $der, $write_data_type)=ReadDataType($data_type);
($write_data_type)=ReadDataType($data_type);
open(OUTPAUP, '>', $file) || die "Unable to open '$file': $!\n";
@@ -394,7 +421,11 @@ sub BuildPAUP
my($haplo);
foreach $haplo (keys %{$hash_haplo}) {
# printf OUTPAUP "H%.3i_m%.3i_c%.3i\t%s%s\n", $hash_haplo->{$haplo}->[2],$hash_haplo->{$haplo}->[1], $hash_haplo->{$haplo}->[0], $haplo, $der; # a modifier si je fais un deuxième fichier de sortie...
- printf OUTPAUP "H%.3i\t%s\n", $hash_haplo->{$haplo}->[2], $haplo;#, $der;
+ if ($data_quali eq "quali") {
+ printf OUTPAUP "H%.3i\t%s\n", $hash_haplo->{$haplo}->[2], $haplo;#, $der;
+ } else {
+ printf OUTPAUP "H%.3i\t%s\n", $hash_haplo->{$haplo}->{"name"}, $haplo;
+ }
}
print OUTPAUP "H000_ancetre [add ancestral haplotype]\n";#$anc\n";
print OUTPAUP ";\n";
@@ -461,6 +492,7 @@ sub main
"data-type" => \$opt_t,
"phylo-prog" => \$opt_p,
"reconstruct-prog" => \$opt_r,
+ "data-quali" => \$opt_q,
);
#getopts('hr:i:j:o:t:p:');
@@ -476,6 +508,7 @@ sub main
"data-type|t=s",
"phylo-prog|p=s",
"reconstruct-prog|r=s",
+ "data-quali|q=s",
) or pod2usage(2);
if (defined($options{"version"})) {
print $0, " version ", $VERSION, "\n";
@@ -527,7 +560,11 @@ sub main
}
if (!$opt_t){
die "Type of data: opt_t (DNA or NUM) not specified!\n"; #il faudra peut-etre vérifier que les données sont bien du bon type???
- }
+ }
+ my $data_quali;
+ if (! $opt_q){
+ die "Data quality: opt_q, (qualitative or quantitative) not specified!\n";
+ }
my($hash_ind, $hash_statut, $hash_haplo);
my($nb_haplo, $nb_loci);
@@ -548,14 +585,23 @@ sub main
} else {
die "Unknown software. Check the -r option! \n";
}
+
+ if ($opt_q =~ /^[Qq][Uu][Aa][Ll][Ii][Tt][Aa][Tt][Ii][Vv][Ee]$/) {
+ $data_quali="quali";
+ } elsif ($opt_q =~ /^[Qq][Uu][Aa][Nn][Tt][Ii][Tt][Aa][Tt][Ii][Vv][Ee]$/) {
+ $data_quali="quanti";
+ } else {
+ die "Unknown data_qual. Check the -q option! \n";
+ }
+
#print_hash_ind($hash_ind);
- ($hash_haplo, $nb_haplo)=TransfoData($hash_ind);
+ ($hash_haplo, $nb_haplo)=TransfoData($hash_ind, $data_quali);
# AfficheHashHaplo($hash_haplo); # pour verifier
if ($phylo_program =~ /^[Pp][Aa][Uu][Pp]$/) {
- BuildPAUP($opt_o, $hash_haplo, $nb_haplo, $nb_loci, $opt_t, $opt_c)
+ BuildPAUP($opt_o, $hash_haplo, $nb_haplo, $nb_loci, $opt_t, $opt_c, $data_quali)
} elsif ($phylo_program =~ /^[Pp][Hh][Yy][Ll][Ii][Pp]$/) {
BuildPHYLIP($opt_o, $hash_haplo, $nb_haplo, $nb_loci, $opt_t, $opt_c);
} else {
--
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