Mercurial > repos > sarahinraauzeville > tax4fun

comparison sm_Tax4Fun.pl @ 9:bd5ba02b1f71 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author sarahinraauzeville
date Thu, 21 Dec 2017 09:08:53 -0500
parents
children
comparison
equal deleted inserted replaced
8:a6a0c9a8ad51 9:bd5ba02b1f71
1 #Declaration de l espace de travail et du chemin de l executable R :
2 use strict;
3 use Carp;
4 use Statistics::R;
5 use Cwd qw(abs_path);
6 use File::Basename;
7 use Getopt::Long;
8
9
10 #Variables Globales ###########################
11 defined $ENV{'MY_GALAXY_DIR'} || die "MY_GALAXY_DIR environment variable not defined";
12 use lib "$ENV{'MY_GALAXY_DIR'}";
13 use GalaxyPath;
14
15 my ($r_bin,$log_dir,$R,$cmd,$line, $out, $input, $reference);
16
17
18 #test:
19 #perl sm_Tax4Fun.pl --input DATA/testtax4fun---ssu---fingerprint----Total---sim_93---tax_silva---td_20.csv --out DATA/Tax4FunProfile.txt
20
21
22 #Parametres d'entree
23 Getopt::Long::Configure( 'no_ignorecase', 'bundling' );
24 GetOptions (
25 'out=s' => \$out,
26 'input=s' => \$input,
27 'reference=s' => \$reference
28 ) or die "Usage: Error in command line arguments\n";
29
30 # SETTING GLOBAL VARIABLES ####################################################
31 my $cfg = GalaxyPath->new( -file => $ENV{"GALAXY_CONFIG_FILE"} );
32 my $file_path = $cfg->my_path( 'workPath', 'MYWORKSPACE' );
33 $r_bin = $cfg->my_path( 'toolsPath', 'R_BIN_PATH' );
34 my $SCRIPTS_R_path = $cfg->my_path( 'toolsPath', 'SCRIPTS_R_path' );
35 ###############################################################################
36
37 #workspace
38 my $debug = 0; #Mode debug (0)
39 if ($debug == 0)
40 {
41 print STDOUT "Debug mode OK \n";
42 }
43 else
44 {
45 $file_path = dirname($out);
46 print STDOUT "No debug \n";
47 }
48
49
50
51 my ($nb) = ($out=~/dataset_(\d+)\.\S+$/);
52 #For debugging in command line on vm-galaxy-preprod
53 #my ($nb) = (1);
54 #creation du repertoire de sortie
55 `cd $file_path; mkdir $nb; chmod -R 777 $nb `;
56 my $dirresults= $file_path."/".$nb;
57
58
59 print STDOUT "Job working directory : $dirresults \n";
60
61
62
63 #remplacer les [a-z]__ du fichier entrant $input par rien
64 #$str =~ s/$find/$replace/g;
65 `cp -a $input $dirresults/INPUT.csv`;
66 open(FILE, "<$dirresults/INPUT.csv") || die "File not found";
67 my @lines = <FILE>;
68 close(FILE);
69
70 my @newlines;
71 my %Taxo=();
72 foreach(@lines) {
73 $_ =~ s/[a-z]\_\_//g; #homogeneiser la taxonomie issues de frogs avec celle utilisée par tax4fun
74 $_ =~ s/\n/;\n/g; #pour qu'il y ait un point virgule a la fin de chaque ligne
75 $_ =~ s/;;/;/g; #remplacer les ;; par un seul ;
76 $_ =~ s/;;/;/g; #remplacer les ;; par un seul ; une seconde fois pour les triples points virgules
77 #push(@newlines,$_);
78 /^(\d+)\t(.+)/||die "bad line: $_";
79 $Taxo{$2}+=$1;
80 }
81
82 open(FILE, ">$dirresults/INPUT.csv") || die "File not found";
83 #print FILE "abondance_sum\tTaxonomy\n";
84 print FILE "abondance_sum;\n";
85 #print FILE @newlines;
86 foreach my $taxo (sort {$a cmp $b} keys %Taxo) {
87 printf FILE "%d\t%s\n",$Taxo{$taxo},$taxo;
88 }
89 close(FILE);
90
91
92 #Log dir
93 $log_dir = $dirresults;
94
95 #déaration de l'objet $R et ouverture du pont :
96 $R = Statistics::R->new(
97 "r_bin" => $r_bin,
98 "log_dir" => $log_dir,
99 ) or die "Problem with R : $!\n";
100 # Ouverture du pont
101 $R->startR;
102
103
104 print STDOUT "Ouverture du pont R \n";
105
106 #Read R script
107 $cmd="";
108 #[galaxy-preprod@vm-galaxy-preprod sm_Tax4Fun]$ ln -s /galaxydata/galaxy-preprod/my_tools/sm_Tax4Fun/sm_Tax4Fun.R /galaxydata/galaxy-preprod/my_bin/scripts_R/.
109 open IN,"< $SCRIPTS_R_path/sm_Tax4Fun.R"
110 or die "Unable to read R script : $!\n";
111 while ($line=<IN>) {
112 $cmd.=$line;
113 }
114 close(IN);
115
116 #Declare R function
117 print STDOUT "Declaration du script R \n";
118
119 #$dirresults/INPUT.csv #"input.file = '$input', ".
120 $R->send(
121 "setwd('$dirresults')\n".
122 "$cmd\n".
123 "GalaxyFrogsTax( ".
124 "input.file = '$dirresults/INPUT.csv', ".
125 "reference = '$reference', ".
126 "output.file = '$out')\n");
127
128 print STDOUT "Envoi du script R ";
129
130
131
132
133 #Fermeture du pont
134 $R->stopR();
135
136 print STDOUT "Fermeture du pont R \n";
137
138 #Recuperation des outputs dans Galaxy
139 my $cmdOUT ='';
140 my $outTax= "$dirresults/Tax4FunProfile.txt";
141 if (! -e $out){print STDERR "Pas de fichier Tax4FunProfile.txt produit \n";}
142 else {$cmdOUT = "(mv $outTax $out) >& ./cp_taxout.log 2>&1";
143 system $cmdOUT;}