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

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author elixir-it
date Wed, 22 Jul 2020 19:20:30 +0000
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1:35c308dd6420 2:6e4eb4856874
1 #!/usr/bin/perl -w
2 #use strict;
3
4 %arguments=
5 (
6 "vcf"=>"", #file mandatory, provided at runtime
7 "disease"=>"", #name optional
8 "similarD"=>"", #file optional
9 "lgenes"=>"", #file optional
10 "leQTL"=>"qfile", #file mandatory, but default value
11 "keywords"=>"kfile", #file mandatory, but default value
12 "effects"=>"efile", #file mandatory, but default value
13 "disease_clinvar"=>8, #numeric mandadory, but default value
14 "score_AF"=>4, #numeric mandatory, but default value
15 "score_functional"=>8, #numeric mandatory, but default value
16 "score_NS"=>6, #numeric mandatory, but default value
17 "score_nIND"=>8, #numeric mandatory, but default value
18 "AF"=>0.0001, #numeric mandatory, but default value
19 "scoreeQTL"=>1, #numeric mandatory, but default value
20 "nind"=>5, #numeric mandatory, but default value
21 "scoreG"=>2, #numeric mandatory, but default value
22 #####OUTPUT file#############################################
23 "ofile"=>"final_res.csv", #file #OUTPUT #tabulare
24 "ovcfile"=>"final_res.vcf" #file #OUTOUT #vcf
25 );
26
27
28 @arguments=@ARGV;
29 for ($i=0;$i<=$#ARGV;$i+=2)
30 {
31 $act=$ARGV[$i];
32 $act=~s/-//g;
33 $val=$ARGV[$i+1];
34 if (exists $arguments{$act})
35 {
36 $arguments{$act}=$val;
37 }else{
38 warn("$act: unknown argument\n");
39 @valid=keys %arguments;
40 warn("Valid arguments are @valid\n");
41 die("All those moments will be lost in time, like tears in rain.\n Time to die!\n");
42 }
43 #print "$act $val\n";
44 }
45
46 $ofile_name=$arguments{"ofile"};
47 open(O,">$ofile_name");
48 $ovcfile=$arguments{"ovcfile"};
49 open(OV,">$ovcfile");
50
51
52 $file=$arguments{"vcf"} ;
53 die ("input file $file not found!\n") unless -e $file;
54
55 $lgenes=$arguments{"lgenes"};
56 if (-e $lgenes)
57 {
58 open(IN,$lgenes);
59 while(<IN>)
60 {
61 chomp;
62 $Lgenes{$_}=1;
63 }
64 }
65
66
67 $kfile=$arguments{"keywords"};
68 die ("keyword file $kfile not found!\n") unless -e $kfile;
69 open(IN,$kfile);
70 while(<IN>)
71 {
72 chomp;
73 $specialKeys{$_}=1;
74 }
75
76
77 $diseaseO=$arguments{"disease"} ? $arguments{"disease"} : "GinocchioValgoDellaLavandaiaZoppa";
78
79 $sfile=$arguments{"similarD"};
80 if (-e $sfile)
81 {
82 open(IN,$sfile);
83 while(<IN>)
84 {
85 chomp;
86 push(@kw,$_)
87 }
88 }
89
90 $efile=$arguments{"effects"};
91 die ("effect file $efile not found!\n") unless -e $efile;
92 open(IN,$efile);
93 while(<IN>)
94 {
95 chomp;
96 $effects{$_}=1;
97 }
98
99 $leQTLfile=$arguments{"leQTL"};
100 if (-e $leQTLfile)
101 {
102 open(IN,$leQTLfile);
103 while(<IN>)
104 {
105 chomp();
106 $Qlist{$_}=1;
107 }
108 }
109
110 $disease_clinvar=$arguments{"disease_clinvar"};
111 $score_AF=$arguments{"score_AF"};
112 $score_functional=$arguments{"score_functional"};
113 $score_NS=$arguments{"score_NS"};
114 $score_nIND=$arguments{"score_nIND"};
115 $score_QTL=$arguments{"scoreeQTL"};
116 $scoreG=$arguments{"scoreG"};
117
118 print O "CHR\tstart\tgene\tref\talt\tAC\t";
119 foreach $k (sort keys %specialKeys)
120 {
121 print O "$k\t";
122 }
123 print O "Score\n";
124
125 %damaged=();
126 open(IN,$file);
127
128 #print "$gene_score $disease_HGMD $disease_clinvar $score_functional $score_AF $score_NS $score_eQTL $score_nIND\n";
129 while(<IN>)
130 {
131 if ($_=~/^#/)
132 {
133 print OV;
134 next;
135 }
136 chomp();
137 @val=(split(/\t/));
138 $chr=$val[0];
139 $start=$val[1];
140 $pstart=$val[2];
141 $b1=$val[3];
142 $b2=$val[4];
143 $qscore=$val[5];
144 $pb2=$val[6];
145 $gene="na";
146 $annot=$val[7];
147 $gt=$val[8];
148 @samples=@val[9..$#val];
149 $samples=(join("\t",@samples));
150 @terms=(split(/\;/,$annot));
151 $DIS=0;
152 if ($_=~/;AC=(\d+);/)
153 {
154 $nind=$1;
155 }
156 if ($_=~/Gene.refGene=(\w+);/)
157 {
158 $gene=$1;
159 }
160 next if $nind==0;
161 $gene=(split(/\,/,$gene))[0];
162 $i=0;
163 %keep=();
164 $score=0;
165 $score+=$scoreG if $Lgenes{$gene};
166 foreach $t (@terms)
167 {
168 ($keep,$value)=(split(/\=/,$t))[0,1];
169 $keep{$keep}=$value;
170 }
171
172 if ($keep{"CLNSIG"} ne "."){
173 $scoreO=0;
174 $scoreC=0;
175 $add=0;
176 $add=$disease_clinvar if ($keep{"CLNSIG"} eq "Pathogenic" || $keep{"CLNSIG"} eq "Pathogenic,_other,_risk_factor" || $keep{"CLNSIG"} eq "pathogenic" || $keep{"CLNSIG"} eq "Pathogenic/Likely_pathogenic" );
177 $add=$disease_clinvar/2 if ($keep{"CLNSIG"} eq "Likely_pathogenic" || $keep{"CLNSIG"} eq "Conflicting_interpretations_of_pathogenicity" || $keep{"CLNSIG"} eq "likely-pathogenic");
178 $add=-$disease_clinvar/2 if ($keep{"CLNSIG"} eq "Likely_benign" || $keep{"CLNSIG"} eq "Benign/Likely_benign");
179 $add=-$disease_clinvar if ($keep{"CLNSIG"} eq "Benign");
180 @diseases=split(/\|/,$keep{"CLNDN"});
181 @databases=split(/\|/,$keep{"CLNDISDB"});
182 for ($i=0;$i<=$#diseases;$i++)
183 {
184 $dis=lc $diseases[$i];
185 $dat=$databases[$i];
186 if ($dis=~ /$diseaseO/)
187 {
188 if ($dat=~/OMIM/)
189 {
190 $scoreO=$add;
191 }else{
192 $scoreC=$add;
193 }
194 last;
195 }else{
196 foreach $kv (@kw)
197 {
198 if ($dis=~/$kv/)
199 {
200 $DIS=1 if $add>0;
201 if ($dat=~/OMIM/)
202 {
203 $scoreO=$add;
204 }else{
205 $scoreC=$add;
206 }
207 }
208 }
209 }
210 }
211 $score+=$scoreO+$scoreC;
212 }
213 $esp=$keep{"esp6500siv2_ea"} eq "." ? 0 : $keep{"esp6500siv2_ea"};
214 $g1000=$keep{"1000g2015aug_all"} eq "." ? 0 : $keep{"1000g2015aug_all"} ;
215 $exac=$keep{"ExAC_NFE"} eq "." ? 0 : $keep{"ExAC_NFE"};
216 $gnomad=$keep{"gnomAD_exome_NFE"} eq "." ? 0 : $keep{"gnomAD_exome_NFE"};
217 @AF=($esp,$g1000,$exac,$gnomad);
218 @AF=sort{$a<=>$b} @AF;
219 $AF=$AF[-1];
220 # Variante molto rara 0.0001 2 punti
221 # Variante rara 0.004 1 punto
222 if ($AF<=$arguments{"AF"}) #0,00002
223 {
224 $score+=$score_AF;
225 }elsif($AF>$arguments{"AF"} && $AF<=$arguments{"AF"}*4){
226 $score+=$score_AF/2;
227 }elsif($AF>0.01){ #commonSNP
228 $score-=$score_AF/2;
229 }
230
231 $effectO=(split(/\;/,$keep{"ExonicFunc.refGene"}))[0];
232 if ($effects{$effectO})
233 {
234 $damaged{$gene}{"D"}++;
235 $score+=$score_functional;
236 }
237 #print "Exon " . $keep{"ExonicFunc.refGene"}. " $score\n";
238 if ($keep{"ExonicFunc.refGene"} eq "nonsynonymous_SNV"){
239
240 if ($keep{"MetaSVM_pred"} eq "D" && $keep{"CADD_raw"}>=5)
241 {
242 $score+=$score_NS;
243 $damaged{$gene}{"D"}++;
244 }elsif($keep{"MetaSVM_pred"} eq "D" && $keep{"CADD_raw"}<5){
245 $score+=$score_NS/2;
246 }elsif($keep{"MetaSVM_pred"} ne "D" && $keep{"CADD_raw"}>=5){
247 $score+=$score_NS/2;
248 }
249 }
250 #print "NS ". $keep{"ExonicFunc.refGene"} . " $score\n";
251 $damaged{$gene}{"tot"}++;
252 if ($keep{"Func.refGene"} eq "splicing"){
253 $score+=$score_functional;
254 }
255 #print "SPL ". $keep{"Func.refGene"} . " $score\n";
256 foreach $QTL (keys %Qlist)
257 {
258 next unless $keep{$QTL};
259 $score+=$score_QTL if ($keep{$QTL} ne ".");
260 }
261 if ($nind>=$arguments{"nind"} && $AF<=0.01)
262 {
263 $score+=$score_nIND;
264 }elsif($nind>=$arguments{"nind"}/2 && $nind<$arguments{"nind"} && $AF<=0.01){
265 $score+=$score_nIND/2;
266 }
267 chomp();
268 #$scores{$score}++;
269 chop($_);
270 $outL="";
271 foreach $k (sort keys %specialKeys)
272 {
273 #die("$k\n") unless $keep{$k};
274 $outL.="$keep{$k}\t";
275 }
276 print O "$chr\t$start\t$gene\t$b1\t$b2\t$nind\t$outL$score\n"; #if $score>=12 || $DIS==1;
277 print OV "$chr\t$start\t$pstart\t$b1\t$b2\t$qscore\t$pb2\t$annot;COSO_score=$score\t$gt\t$samples\n";
278 }
279 #open(O,">$file.gc.list.csv");
280 #foreach $gene (sort{$a<=>$b} keys %G)
281 #{
282 # $pos=$G{$gene}{"GR"} ? $G{$gene}{"GR"} : 0;
283 # $neg=$G{$gene}{"LW"} ? $G{$gene}{"LW"} : 0;
284 #print O "$gene $pos $neg\n";
285 ##$Tscore+=$scores{$score} if $score>=$coff;
286 #}
287
288 #open(D,">$file\_damaged.csv");
289 #foreach $gene (sort{$a<=>$b} keys %damaged)
290 #{
291 # $D=$damaged{$gene}{"D"} ? $damaged{$gene}{"D"} : 0;
292 # $T=$damaged{$gene}{"tot"};
293 #print D "$gene $D $T\n";
294 #}
295
296 #print "$Tscore\n";