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Changeset 9:bd5ba02b1f71 (2017-12-21)

Previous changeset 8:a6a0c9a8ad51 (2017-12-21) Next changeset 10:444f1e7fe177 (2017-12-21)

Commit message:
Uploaded

added:
sm_Tax4Fun.pl

diff -r a6a0c9a8ad51 -r bd5ba02b1f71 sm_Tax4Fun.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sm_Tax4Fun.pl Thu Dec 21 09:08:53 2017 -0500

[

@@ -0,0 +1,143 @@
+#Declaration de l espace de travail et du chemin de l executable R :
+use strict;
+use Carp;
+use Statistics::R;
+use Cwd qw(abs_path);
+use File::Basename;
+use Getopt::Long;
+
+
+#Variables Globales ###########################
+defined $ENV{'MY_GALAXY_DIR'} || die "MY_GALAXY_DIR environment variable not defined";
+use lib "$ENV{'MY_GALAXY_DIR'}";
+use GalaxyPath;
+
+my ($r_bin,$log_dir,$R,$cmd,$line, $out, $input, $reference);
+
+
+#test:
+#perl sm_Tax4Fun.pl --input DATA/testtax4fun---ssu---fingerprint----Total---sim_93---tax_silva---td_20.csv --out DATA/Tax4FunProfile.txt
+
+
+#Parametres d'entree
+Getopt::Long::Configure( 'no_ignorecase', 'bundling' );
+GetOptions (
+    'out=s' => \$out,
+    'input=s' => \$input,
+    'reference=s' => \$reference
+) or die "Usage: Error in command line arguments\n";
+
+# SETTING GLOBAL VARIABLES ####################################################
+my $cfg = GalaxyPath->new( -file => $ENV{"GALAXY_CONFIG_FILE"} );
+my $file_path = $cfg->my_path( 'workPath', 'MYWORKSPACE' );
+$r_bin = $cfg->my_path( 'toolsPath', 'R_BIN_PATH' );
+my $SCRIPTS_R_path = $cfg->my_path( 'toolsPath', 'SCRIPTS_R_path' );
+###############################################################################
+
+#workspace
+my $debug = 0; #Mode debug (0)
+if ($debug == 0)
+ {
+ print STDOUT "Debug mode OK \n";
+ }
+else
+ {
+ $file_path = dirname($out);
+ print STDOUT "No debug \n";
+ }
+
+
+
+my ($nb) = ($out=~/dataset_(\d+)\.\S+$/);
+#For debugging in command line on vm-galaxy-preprod
+#my ($nb) = (1);
+#creation du repertoire de sortie
+`cd $file_path; mkdir $nb; chmod -R 777 $nb `;
+my $dirresults= $file_path."/".$nb;
+
+
+print STDOUT "Job working directory : $dirresults \n";
+
+
+
+#remplacer les [a-z]__ du fichier entrant $input par rien
+#$str =~ s/$find/$replace/g;
+`cp -a $input $dirresults/INPUT.csv`;
+open(FILE, "<$dirresults/INPUT.csv") || die "File not found";
+my @lines = <FILE>;
+close(FILE);
+
+my @newlines;
+my %Taxo=();
+foreach(@lines) {
+   $_ =~ s/[a-z]\_\_//g;   #homogeneiser la taxonomie issues de frogs avec celle utilisée par tax4fun
+   $_ =~ s/\n/;\n/g;       #pour qu'il y ait un point virgule a la fin de chaque ligne
+   $_ =~ s/;;/;/g;         #remplacer les ;; par un seul ;
+   $_ =~ s/;;/;/g;         #remplacer les ;; par un seul ; une seconde fois pour les triples points virgules
+   #push(@newlines,$_);
+   /^(\d+)\t(.+)/||die "bad line: $_";
+   $Taxo{$2}+=$1;
+}
+
+open(FILE, ">$dirresults/INPUT.csv") || die "File not found";
+#print FILE "abondance_sum\tTaxonomy\n";
+print FILE "abondance_sum;\n";
+#print FILE @newlines;
+foreach my $taxo (sort {$a cmp $b} keys %Taxo) {
+    printf FILE "%d\t%s\n",$Taxo{$taxo},$taxo;
+}
+close(FILE);
+
+
+#Log dir
+$log_dir = $dirresults;
+
+#déaration de l'objet $R et ouverture du pont :
+$R = Statistics::R->new(
+    "r_bin"   => $r_bin,
+    "log_dir" => $log_dir,
+) or die "Problem with R : $!\n";
+# Ouverture du pont
+$R->startR;
+
+
+print STDOUT "Ouverture du pont R \n";
+
+#Read R script
+$cmd="";
+#[galaxy-preprod@vm-galaxy-preprod sm_Tax4Fun]$ ln -s /galaxydata/galaxy-preprod/my_tools/sm_Tax4Fun/sm_Tax4Fun.R /galaxydata/galaxy-preprod/my_bin/scripts_R/.
+open IN,"< $SCRIPTS_R_path/sm_Tax4Fun.R"
+ or die "Unable to read R script : $!\n";
+while ($line=<IN>) {
+ $cmd.=$line;
+}
+close(IN);
+
+#Declare R function
+print STDOUT "Declaration du script R \n";
+
+#$dirresults/INPUT.csv  #"input.file = '$input', ".
+$R->send(
+     "setwd('$dirresults')\n".
+     "$cmd\n".
+     "GalaxyFrogsTax( ".
+     "input.file = '$dirresults/INPUT.csv', ".
+     "reference = '$reference', ".
+     "output.file = '$out')\n");
+
+print STDOUT "Envoi du script R ";
+
+
+
+
+#Fermeture du pont
+$R->stopR();
+
+print STDOUT "Fermeture du pont R \n";
+
+#Recuperation des outputs dans Galaxy
+my $cmdOUT ='';
+my $outTax= "$dirresults/Tax4FunProfile.txt";
+if (! -e $out){print STDERR "Pas de fichier Tax4FunProfile.txt produit \n";}
+else {$cmdOUT = "(mv $outTax $out) >& ./cp_taxout.log 2>&1";
+system $cmdOUT;}