Mercurial > repos > elixir-it > vinyl_optimizer

comparison old_version/optimizer_M.pl @ 2:6e4eb4856874 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Wed, 22 Jul 2020 19:20:30 +0000
parents
children
comparison
equal deleted inserted replaced
1:35c308dd6420 2:6e4eb4856874
1 #!/usr/bin/perl -w
2 use Cwd;
3 use strict;
4
5 my %arguments=
6 (
7 "fileR"=>"", #file: vcf file of affected individuals
8 "fileC"=>"", #file: vcf file of unaffected individuals
9 "ofile"=>"", #name: name of the output files
10 "AD"=>"T",
11 "XL"=>"F", #
12 "disease_clinvar"=>[4,6], #numeric mandadory, multiple values
13 "score_AF"=>[2,4], #numeric mandatory, multiple values
14 "score_functional"=>[4,6], #numeric mandatory, multiple values
15 "score_NS"=>[2,4], #numeric mandatory, multiple values
16 "score_nIND"=>[2,4], #numeric mandatory, multiple values
17 "scoreeQTL"=>[2,4], #numeric mandatory, multiple values
18 "scoreG"=>[3,5], #numeric mandatory, multiple values
19 "scoreI"=>[0.1..0.3],
20 "disease"=>"", #name optional
21 "similarD"=>"", #file optional
22 "lgenes"=>"", #file optional
23 "leQTL"=>"qfile", #file mandatory, but default value
24 "keywords"=>"kfile", #file mandatory, but default value
25 "effects"=>"efile", #file mandatory, but default value
26 "ifile"=>"inter_Hs.file",
27 "nind"=>5,
28 "AF"=>0.0001
29 );
30
31 my @arguments=@ARGV;
32 for (my $i=0;$i<=$#ARGV;$i+=2)
33 {
34 my $act=$ARGV[$i];
35 $act=~s/-//g;
36 my $val=$ARGV[$i+1];
37 if (exists $arguments{$act})
38 {
39 unless ($val=~/\:/)
40 {
41 $arguments{$act}=$val;
42 }else{
43 my ($s,$e)=(split(/\:/,$val));
44 my $increment= $s=~/\./ ? 0.1 : 1;
45 my @vls=();
46 for (my $I=$s;$I<=$e;$I+=$increment)
47 {
48 push(@vls,$I);
49 }
50 $arguments{$act}=\@vls;
51 }
52 }else{
53 warn("$act: unknown argument\n");
54 my @valid=keys %arguments;
55 warn("Valid arguments are @valid\n");
56 die("All those moments will be lost in time, like tears in rain.\n Time to die!\n");
57 }
58 #print "$act $val\n";
59 }
60
61 my %compose_ARG=
62 (
63 "disease"=>1, #name optional
64 "similarD"=>1, #file optional
65 "lgenes"=>1, #file optional
66 "leQTL"=>1, #file mandatory, but default value
67 "keywords"=>1, #file mandatory, but default value
68 "effects"=>1, #file
69 "AF"=>1,
70 "nind"=>1,
71 "AD"=>1,
72 "XL"=>1,
73 "ifile"=>1
74
75 );
76
77 my $dir=getcwd();
78 my $add_string=" ";
79
80 foreach my $a (keys %compose_ARG)
81 {
82 $add_string.="-$a $arguments{$a} " if $arguments{$a} ne "";
83 }
84
85
86 my @DC=@{$arguments{"disease_clinvar"}}; #=>[2..8], #numeric mandadory, but default value
87 my @AF=@{$arguments{"score_AF"}}; #numeric mandatory, but default value
88 my @FUN=@{$arguments{"score_functional"}}; #=>[2..8], #numeric mandatory, but default value
89 my @NS=@{$arguments{"score_NS"}}; #=>[2..8], #numeric mandatory, but default value
90 my @NI=@{$arguments{"score_nIND"}}; #=>[2..8], #numeric mandatory, but default value
91 my @Q=@{$arguments{"scoreeQTL"}}; #numeric mandatory, but default value
92 my @G=@{$arguments{"scoreG"}}; #=>[1..3], #numeric mandatory, but default value
93 my @I=@{$arguments{"scoreI"}};
94
95 my $Rfile=$arguments{"fileR"};
96 my $Tfile=$arguments{"fileC"};
97 my $Ofile=$arguments{"ofile"};
98
99 #print "@DC\n @AF\n @FUN\n @NS\n @NI\n @Q\n @G\n @I\n";
100
101 open(O,">$Ofile");
102 print O "score_DB\tscore_RV\tscore_FE\tscore_NS\tscore_OR\tscore_eQ\tscore_AD\tScore_DG\tCut_Off\tPos_Affected\tPos_Healthy\tPvalue\tFold_change\n";
103
104
105 my $commandR="perl $dir/score_complete_alt_M.pl -vcf $dir/$Rfile -ofile $dir/R.csv -ovcfile $dir/R.vcf $add_string";
106 my $commandT="perl $dir/score_complete_alt_M.pl -vcf $dir/$Tfile -ofile $dir/T.csv -ovcfile $dir/T.vcf $add_string";
107 my %ODATA=();
108
109 foreach my $dc (@DC)
110 {
111
112 foreach my $af (@AF)
113 {
114
115 foreach my $fun (@FUN)
116 {
117
118 foreach my $ns (@NS)
119 {
120
121 foreach my $ni (@NI)
122 {
123
124
125 foreach my $Q (@Q)
126 {
127 foreach my $G (@G)
128 {
129 foreach my $I (@I)
130 {
131 $commandR.="-score_AF $af ";
132 $commandT.="-score_AF $af ";
133 $commandR.="-score_functional $fun ";
134 $commandT.="-score_functional $fun ";
135 $commandR.="-score_NS $ns ";
136 $commandT.="-score_NS $ns ";
137 $commandR.="-score_nIND $ni ";
138 $commandT.="-score_nIND $ni ";
139 $commandR.="-scoreeQTL $Q ";
140 $commandT.="-scoreeQTL $Q ";
141 $commandR.="-disease_clinvar $dc ";
142 $commandT.="-disease_clinvar $dc ";
143 $commandR.="-scoreG $G ";
144 $commandT.="-scoreG $G ";
145 $commandR.="-scoreI $I ";
146 $commandT.="-scoreI $I ";
147
148 system($commandR)==0||die("Non giro Rfile");
149 system($commandT)==0||die("Non giro Tfile");
150 $commandR="perl $dir/score_complete_alt_M.pl -vcf $dir/$Rfile -ofile $dir/R.csv -ovcfile $dir/R.vcf $add_string";
151 $commandT="perl $dir/score_complete_alt_M.pl -vcf $dir/$Tfile -ofile $dir/T.csv -ovcfile $dir/T.vcf $add_string";
152 my $r=`Rscript --vanilla $dir/wilcox.R $dir/R.csv $dir/T.csv`;
153 my $PV=(split(/\t/,$r))[3];
154 push(@{$ODATA{$PV}},"$dc\t$af\t$fun\t$ns\t$ni\t$Q\t$G\t$I\t$r\n");
155 }
156 }
157 }
158 }
159 }
160 }
161 }
162 }
163
164 foreach my $O (sort {$a<=>$b} keys %ODATA)
165 {
166 my @values=@{$ODATA{$O}};
167 foreach my $v (@values)
168 {
169 print O "$v";
170 }
171 }