master
parent
6a22cb8463
commit
11fac53bdb
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@ -17,7 +17,6 @@ open LONGINDEL, "> $out";
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my ($longindel) = info();
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my @longindels = @$longindel;
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my @pos;
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my $h2;
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while (<IN>) {
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@ -25,20 +24,24 @@ while (<IN>) {
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next if /^##/;
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if (/^#CHROM/) {
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$h2 = $_;
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print LONGINDEL "$h2\n";
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print LONGINDEL "$h2\tHGVS\tfreq\n";
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next;
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}
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my @line = split(/\t/);
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$line[7] =~ /Gene.refGene=(.*?);/;
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my $gene = $1;
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if ((grep {$gene =~ /$_/} @longindels) && ($_ =~ /SVTYPE=DEL/ || $_ =~ /SVTYPE=DUP/ || $_ =~ /SVTYPE=INS/)) {
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my $freq = (split(/:/, $line[9]))[9] / (split(/:/, $line[9]))[7];
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my $hgvs = '.';
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if ($gene eq "BCL2L11") {
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if ($line[1] == '111883194') {
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print LONGINDEL $_;
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$hgvs = "BCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del";
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print LONGINDEL $_ . "\t$hgvs\t$freq\n";
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}
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}
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else {
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print LONGINDEL $_;
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print LONGINDEL $_ . "\t$hgvs\t$freq\n";
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}
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}
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}
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@ -477,7 +477,7 @@ class PostProcess:
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# 添加常规列
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filter_sum_pos_df = self._add_columns(filter_sum_pos_df)
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# 添加基因功能
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filter_sum_pos_df = self._add_gene_function(filter_sum_pos_df, colname='ref_gene')
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filter_sum_pos_df = self._add_gene_function(filter_sum_pos_df, colname='Gene_Symbol')
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# 药物处理
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self.drug_parse(filter_sum_pos_df['DrugCn'].to_list())
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filter_sum_pos_df['Validated'] = 1
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -1,128 +1,131 @@
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chr1 2488152 2488153
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chr1 23885598 23885599
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chr1 65321387 65321388
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chr1 120612005 120612006
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chr1 193094374 193094375
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chr1 226570839 226570840
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chr2 47693958 47693959
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chr2 48030837 48030838
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chr2 61749715 61749716
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chr2 141032087 141032088
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chr2 215645463 215645464
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chr3 30686413 30686414
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chr3 47125384 47125385
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chr3 134644635 134644636
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chr3 142281611 142281612
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chr3 192053273 192053274
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chr4 55599435 55599436
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chr4 143007418 143007419
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chr4 153252060 153252061
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chr4 185310217 185310218
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chr4 25666098 25666099
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chr5 35857176 35857177
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chr5 38955795 38955796
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chr5 39074295 39074296
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chr5 67522721 67522722
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chr5 112162853 112162854
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chr5 149435758 149435759
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chr5 161119124 161119125
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chr5 170819886 170819887
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chr5 180046343 180046344
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chr6 30858856 30858857
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chr6 32797875 32797876
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chr6 36645695 36645696
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chr6 117678082 117678083
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chr6 117714345 117714346
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chr7 2946460 2946461
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chr7 2962752 2962753
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chr7 87138644 87138645
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chr7 151970930 151970931
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chr8 90955623 90955624
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chr8 90970934 90970935
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chr8 90995018 90995019
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chr8 68864727 68864728
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chr8 38322345 38322346
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chr8 145742878 145742879
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chr9 5081779 5081780
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chr9 8389363 8389364
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chr9 93657760 93657761
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chr9 98209593 98209594
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chr9 21991922 21991923
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chr9 37020621 37020622
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chr9 21975016 21975017
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chr10 43600688 43600689
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chr10 89720906 89720907
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chr10 104596980 104596981
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chr10 104849467 104849468
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chr10 104855655 104855656
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chr10 123239111 123239112
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chr11 32410773 32410774
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chr11 69462909 69462910
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chr11 94197259 94197260
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chr11 94225806 94225807
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chr11 94225919 94225920
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chr11 125497465 125497466
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chr12 1040372 1040373
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chr12 4553382 4553383
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chr12 6711146 6711147
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chr12 21331624 21331625
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chr12 49427651 49427652
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chr12 49444544 49444545
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chr12 121416621 121416622
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chr12 133202214 133202215
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chr13 21562947 21562948
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chr13 28609824 28609825
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chr13 32936645 32936646
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chr13 113889473 113889474
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chr13 113907390 113907391
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chr14 105239893 105239894
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chr14 105246324 105246325
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chr14 38064214 38064215
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chr14 20820536 20820537
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chr14 35871216 35871217
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chr15 41865487 41865488
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chr15 51502985 51502986
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chr15 51529111 51529112
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chr15 99456252 99456253
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chr15 99478224 99478225
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chr15 51558730 51558731
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chr16 68857440 68857441
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chr16 359952 359953
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chr16 89805976 89805977
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chr16 89838077 89838078
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chr16 89857963 89857964
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chr17 7983968 7983969
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chr17 29486151 29486152
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chr17 29508774 29508775
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chr17 29546174 29546175
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chr17 29559931 29559932
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chr17 29653292 29653293
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chr17 37879761 37879762
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chr17 62007497 62007498
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chr17 78919557 78919558
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chr19 3110348 3110349
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chr19 3119238 3119239
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chr19 4101061 4101062
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chr19 11136214 11136215
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chr19 15289612 15289613
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chr19 15295133 15295134
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chr19 41725270 41725271
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chr20 43956526 43956527
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chr20 43956635 43956636
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chr20 43958849 43958850
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chr20 43958871 43958872
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chr20 54959295 54959296
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chr20 54961540 54961541
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chr21 37518705 37518706
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chr21 39752672 39752673
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chr21 39753374 39753375
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chr22 41568479 41568480
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chr22 30038151 30038152
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chr22 30079212 30079213
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chrX 76937962 76937963
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chrX 39922358 39922359
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chrX 39932906 39932907
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chrX 44938562 44938563
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chrX 100608190 100608191
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chrX 100611284 100611285
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chrX 76940533 76940534
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chr1 2488152 2488153
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chr1 23885598 23885599
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chr1 65321387 65321388
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chr1 120612005 120612006
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chr1 193094374 193094375
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chr1 226570839 226570840
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chr2 47693958 47693959
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chr2 48030837 48030838
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chr2 61749715 61749716
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chr2 141032087 141032088
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chr2 215645463 215645464
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chr3 30686413 30686414
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chr3 47125384 47125385
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chr3 134644635 134644636
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chr3 142281611 142281612
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chr3 192053273 192053274
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chr4 55599435 55599436
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chr4 143007418 143007419
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chr4 153252060 153252061
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chr4 185310217 185310218
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chr4 25666098 25666099
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chr5 35857176 35857177
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chr5 38955795 38955796
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chr5 39074295 39074296
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chr5 67522721 67522722
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chr5 112162853 112162854
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chr5 149435758 149435759
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chr5 161119124 161119125
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chr5 170819886 170819887
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chr5 180046343 180046344
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chr6 30858856 30858857
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chr6 32797875 32797876
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chr6 36645695 36645696
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chr6 117678082 117678083
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chr6 117714345 117714346
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chr7 2946460 2946461
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chr7 2962752 2962753
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chr7 87138644 87138645
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chr7 151970930 151970931
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chr8 90955623 90955624
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chr8 90970934 90970935
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chr8 90995018 90995019
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chr8 68864727 68864728
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chr8 38322345 38322346
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chr8 145742878 145742879
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chr9 5081779 5081780
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chr9 8389363 8389364
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chr9 93657760 93657761
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chr9 98209593 98209594
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chr9 21991922 21991923
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chr9 37020621 37020622
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chr9 21975016 21975017
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chr10 43600688 43600689
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chr10 89720906 89720907
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chr10 104596980 104596981
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chr10 104849467 104849468
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chr10 104855655 104855656
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chr10 123239111 123239112
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chr11 32410773 32410774
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chr11 69462909 69462910
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chr11 94197259 94197260
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chr11 94225806 94225807
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chr11 94225919 94225920
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chr11 125497465 125497466
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chr12 1040372 1040373
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chr12 4553382 4553383
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chr12 6711146 6711147
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chr12 21331624 21331625
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chr12 49427651 49427652
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chr12 49444544 49444545
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chr12 121416621 121416622
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chr12 133202214 133202215
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chr13 21562947 21562948
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chr13 28609824 28609825
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chr13 32936645 32936646
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chr13 113889473 113889474
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chr13 113907390 113907391
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chr14 105239893 105239894
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chr14 105246324 105246325
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chr14 38064214 38064215
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chr14 20820536 20820537
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chr14 35871216 35871217
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chr15 41865487 41865488
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chr15 51502985 51502986
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chr15 51529111 51529112
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chr15 99456252 99456253
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chr15 99478224 99478225
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chr15 51558730 51558731
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chr16 68857440 68857441
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chr16 359952 359953
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chr16 89805976 89805977
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chr16 89838077 89838078
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chr16 89857963 89857964
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chr17 7983968 7983969
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chr17 29486151 29486152
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chr17 29508774 29508775
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chr17 29546174 29546175
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chr17 29559931 29559932
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chr17 29653292 29653293
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chr17 37879761 37879762
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chr17 62007497 62007498
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chr17 78919557 78919558
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chr19 3110348 3110349
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chr19 3119238 3119239
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chr19 4101061 4101062
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chr19 11136214 11136215
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chr19 15289612 15289613
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chr19 15295133 15295134
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chr19 41725270 41725271
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chr20 43956526 43956527
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chr20 43956635 43956636
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chr20 43958849 43958850
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chr20 43958871 43958872
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chr20 54959295 54959296
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chr20 54961540 54961541
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chr21 37518705 37518706
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chr21 39752672 39752673
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chr21 39753374 39753375
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chr22 41568479 41568480
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chr22 30038151 30038152
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chr22 30079212 30079213
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chrX 39932906 39932907
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chrX 44938562 44938563
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chrX 76937962 76937963
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chrX 76940533 76940534
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chrX 100608190 100608191
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chrX 100611284 100611285
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chrX 44833840 44833841
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chrX 53228147 53228148
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chrX 44929076 44929077
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chrX 47424614 47424615
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File diff suppressed because it is too large
Load Diff
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@ -1,128 +1,131 @@
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chr1 2488152 2488153
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chr1 23885598 23885599
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chr1 65321387 65321388
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chr1 120612005 120612006
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chr1 193094374 193094375
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chr1 226570839 226570840
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chr2 47693958 47693959
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chr2 48030837 48030838
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chr2 61749715 61749716
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chr2 141032087 141032088
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chr2 215645463 215645464
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chr3 30686413 30686414
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chr3 47125384 47125385
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chr3 134644635 134644636
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chr3 142281611 142281612
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chr3 192053273 192053274
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chr4 55599435 55599436
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chr4 143007418 143007419
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chr4 153252060 153252061
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chr4 185310217 185310218
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chr4 25666098 25666099
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chr5 35857176 35857177
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chr5 38955795 38955796
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chr5 39074295 39074296
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chr5 67522721 67522722
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chr5 112162853 112162854
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chr5 149435758 149435759
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chr5 161119124 161119125
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chr5 170819886 170819887
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chr5 180046343 180046344
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chr6 30858856 30858857
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chr6 32797875 32797876
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chr6 36645695 36645696
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chr6 117678082 117678083
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chr6 117714345 117714346
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chr7 2946460 2946461
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chr7 2962752 2962753
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chr7 87138644 87138645
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chr7 151970930 151970931
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chr8 90955623 90955624
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chr8 90970934 90970935
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chr8 90995018 90995019
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chr8 68864727 68864728
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chr8 38322345 38322346
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chr8 145742878 145742879
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chr9 5081779 5081780
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chr9 8389363 8389364
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chr9 93657760 93657761
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chr9 98209593 98209594
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chr9 21991922 21991923
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chr9 37020621 37020622
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chr9 21975016 21975017
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chr10 43600688 43600689
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chr10 89720906 89720907
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chr10 104596980 104596981
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chr10 104849467 104849468
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chr10 104855655 104855656
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chr10 123239111 123239112
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chr11 32410773 32410774
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chr11 69462909 69462910
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chr11 94197259 94197260
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chr11 94225806 94225807
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chr11 94225919 94225920
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chr11 125497465 125497466
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chr12 1040372 1040373
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chr12 4553382 4553383
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chr12 6711146 6711147
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chr12 21331624 21331625
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chr12 49427651 49427652
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chr12 49444544 49444545
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chr12 121416621 121416622
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chr12 133202214 133202215
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chr13 21562947 21562948
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chr13 28609824 28609825
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chr13 32936645 32936646
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chr13 113889473 113889474
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chr13 113907390 113907391
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chr14 105239893 105239894
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chr14 105246324 105246325
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chr14 38064214 38064215
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chr14 20820536 20820537
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chr14 35871216 35871217
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chr15 41865487 41865488
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chr15 51502985 51502986
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chr15 51529111 51529112
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chr15 99456252 99456253
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chr15 99478224 99478225
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chr15 51558730 51558731
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chr16 68857440 68857441
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chr16 359952 359953
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chr16 89805976 89805977
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chr16 89838077 89838078
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chr16 89857963 89857964
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chr17 7983968 7983969
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chr17 29486151 29486152
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chr17 29508774 29508775
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chr17 29546174 29546175
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chr17 29559931 29559932
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chr17 29653292 29653293
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chr17 37879761 37879762
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chr17 62007497 62007498
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chr17 78919557 78919558
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chr19 3110348 3110349
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chr19 3119238 3119239
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chr19 4101061 4101062
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chr19 11136214 11136215
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chr19 15289612 15289613
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chr19 15295133 15295134
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chr19 41725270 41725271
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chr20 43956526 43956527
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chr20 43956635 43956636
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chr20 43958849 43958850
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chr20 43958871 43958872
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chr20 54959295 54959296
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chr20 54961540 54961541
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chr21 37518705 37518706
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chr21 39752672 39752673
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chr21 39753374 39753375
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chr22 41568479 41568480
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chr22 30038151 30038152
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chr22 30079212 30079213
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chrX 76937962 76937963
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chrX 39922358 39922359
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chrX 39932906 39932907
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chrX 44938562 44938563
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chrX 100608190 100608191
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chrX 100611284 100611285
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chrX 76940533 76940534
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chr1 2488152 2488153
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chr1 23885598 23885599
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chr1 65321387 65321388
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chr1 120612005 120612006
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chr1 193094374 193094375
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chr1 226570839 226570840
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chr2 47693958 47693959
|
||||
chr2 48030837 48030838
|
||||
chr2 61749715 61749716
|
||||
chr2 141032087 141032088
|
||||
chr2 215645463 215645464
|
||||
chr3 30686413 30686414
|
||||
chr3 47125384 47125385
|
||||
chr3 134644635 134644636
|
||||
chr3 142281611 142281612
|
||||
chr3 192053273 192053274
|
||||
chr4 55599435 55599436
|
||||
chr4 143007418 143007419
|
||||
chr4 153252060 153252061
|
||||
chr4 185310217 185310218
|
||||
chr4 25666098 25666099
|
||||
chr5 35857176 35857177
|
||||
chr5 38955795 38955796
|
||||
chr5 39074295 39074296
|
||||
chr5 67522721 67522722
|
||||
chr5 112162853 112162854
|
||||
chr5 149435758 149435759
|
||||
chr5 161119124 161119125
|
||||
chr5 170819886 170819887
|
||||
chr5 180046343 180046344
|
||||
chr6 30858856 30858857
|
||||
chr6 32797875 32797876
|
||||
chr6 36645695 36645696
|
||||
chr6 117678082 117678083
|
||||
chr6 117714345 117714346
|
||||
chr7 2946460 2946461
|
||||
chr7 2962752 2962753
|
||||
chr7 87138644 87138645
|
||||
chr7 151970930 151970931
|
||||
chr8 90955623 90955624
|
||||
chr8 90970934 90970935
|
||||
chr8 90995018 90995019
|
||||
chr8 68864727 68864728
|
||||
chr8 38322345 38322346
|
||||
chr8 145742878 145742879
|
||||
chr9 5081779 5081780
|
||||
chr9 8389363 8389364
|
||||
chr9 93657760 93657761
|
||||
chr9 98209593 98209594
|
||||
chr9 21991922 21991923
|
||||
chr9 37020621 37020622
|
||||
chr9 21975016 21975017
|
||||
chr10 43600688 43600689
|
||||
chr10 89720906 89720907
|
||||
chr10 104596980 104596981
|
||||
chr10 104849467 104849468
|
||||
chr10 104855655 104855656
|
||||
chr10 123239111 123239112
|
||||
chr11 32410773 32410774
|
||||
chr11 69462909 69462910
|
||||
chr11 94197259 94197260
|
||||
chr11 94225806 94225807
|
||||
chr11 94225919 94225920
|
||||
chr11 125497465 125497466
|
||||
chr12 1040372 1040373
|
||||
chr12 4553382 4553383
|
||||
chr12 6711146 6711147
|
||||
chr12 21331624 21331625
|
||||
chr12 49427651 49427652
|
||||
chr12 49444544 49444545
|
||||
chr12 121416621 121416622
|
||||
chr12 133202214 133202215
|
||||
chr13 21562947 21562948
|
||||
chr13 28609824 28609825
|
||||
chr13 32936645 32936646
|
||||
chr13 113889473 113889474
|
||||
chr13 113907390 113907391
|
||||
chr14 105239893 105239894
|
||||
chr14 105246324 105246325
|
||||
chr14 38064214 38064215
|
||||
chr14 20820536 20820537
|
||||
chr14 35871216 35871217
|
||||
chr15 41865487 41865488
|
||||
chr15 51502985 51502986
|
||||
chr15 51529111 51529112
|
||||
chr15 99456252 99456253
|
||||
chr15 99478224 99478225
|
||||
chr15 51558730 51558731
|
||||
chr16 68857440 68857441
|
||||
chr16 359952 359953
|
||||
chr16 89805976 89805977
|
||||
chr16 89838077 89838078
|
||||
chr16 89857963 89857964
|
||||
chr17 7983968 7983969
|
||||
chr17 29486151 29486152
|
||||
chr17 29508774 29508775
|
||||
chr17 29546174 29546175
|
||||
chr17 29559931 29559932
|
||||
chr17 29653292 29653293
|
||||
chr17 37879761 37879762
|
||||
chr17 62007497 62007498
|
||||
chr17 78919557 78919558
|
||||
chr19 3110348 3110349
|
||||
chr19 3119238 3119239
|
||||
chr19 4101061 4101062
|
||||
chr19 11136214 11136215
|
||||
chr19 15289612 15289613
|
||||
chr19 15295133 15295134
|
||||
chr19 41725270 41725271
|
||||
chr20 43956526 43956527
|
||||
chr20 43956635 43956636
|
||||
chr20 43958849 43958850
|
||||
chr20 43958871 43958872
|
||||
chr20 54959295 54959296
|
||||
chr20 54961540 54961541
|
||||
chr21 37518705 37518706
|
||||
chr21 39752672 39752673
|
||||
chr21 39753374 39753375
|
||||
chr22 41568479 41568480
|
||||
chr22 30038151 30038152
|
||||
chr22 30079212 30079213
|
||||
chrX 39932906 39932907
|
||||
chrX 44938562 44938563
|
||||
chrX 76937962 76937963
|
||||
chrX 76940533 76940534
|
||||
chrX 100608190 100608191
|
||||
chrX 100611284 100611285
|
||||
chrX 44833840 44833841
|
||||
chrX 53228147 53228148
|
||||
chrX 44929076 44929077
|
||||
chrX 47424614 47424615
|
||||
|
|
|
|||
|
|
@ -1,128 +1,131 @@
|
|||
chr1 2488152 2488153
|
||||
chr1 23885598 23885599
|
||||
chr1 65321387 65321388
|
||||
chr1 120612005 120612006
|
||||
chr1 193094374 193094375
|
||||
chr1 226570839 226570840
|
||||
chr2 47693958 47693959
|
||||
chr2 48030837 48030838
|
||||
chr2 61749715 61749716
|
||||
chr2 141032087 141032088
|
||||
chr2 215645463 215645464
|
||||
chr3 30686413 30686414
|
||||
chr3 47125384 47125385
|
||||
chr3 134644635 134644636
|
||||
chr3 142281611 142281612
|
||||
chr3 192053273 192053274
|
||||
chr4 55599435 55599436
|
||||
chr4 143007418 143007419
|
||||
chr4 153252060 153252061
|
||||
chr4 185310217 185310218
|
||||
chr4 25666098 25666099
|
||||
chr5 35857176 35857177
|
||||
chr5 38955795 38955796
|
||||
chr5 39074295 39074296
|
||||
chr5 67522721 67522722
|
||||
chr5 112162853 112162854
|
||||
chr5 149435758 149435759
|
||||
chr5 161119124 161119125
|
||||
chr5 170819886 170819887
|
||||
chr5 180046343 180046344
|
||||
chr6 30858856 30858857
|
||||
chr6 32797875 32797876
|
||||
chr6 36645695 36645696
|
||||
chr6 117678082 117678083
|
||||
chr6 117714345 117714346
|
||||
chr7 2946460 2946461
|
||||
chr7 2962752 2962753
|
||||
chr7 87138644 87138645
|
||||
chr7 151970930 151970931
|
||||
chr8 90955623 90955624
|
||||
chr8 90970934 90970935
|
||||
chr8 90995018 90995019
|
||||
chr8 68864727 68864728
|
||||
chr8 38322345 38322346
|
||||
chr8 145742878 145742879
|
||||
chr9 5081779 5081780
|
||||
chr9 8389363 8389364
|
||||
chr9 93657760 93657761
|
||||
chr9 98209593 98209594
|
||||
chr9 21991922 21991923
|
||||
chr9 37020621 37020622
|
||||
chr9 21975016 21975017
|
||||
chr10 43600688 43600689
|
||||
chr10 89720906 89720907
|
||||
chr10 104596980 104596981
|
||||
chr10 104849467 104849468
|
||||
chr10 104855655 104855656
|
||||
chr10 123239111 123239112
|
||||
chr11 32410773 32410774
|
||||
chr11 69462909 69462910
|
||||
chr11 94197259 94197260
|
||||
chr11 94225806 94225807
|
||||
chr11 94225919 94225920
|
||||
chr11 125497465 125497466
|
||||
chr12 1040372 1040373
|
||||
chr12 4553382 4553383
|
||||
chr12 6711146 6711147
|
||||
chr12 21331624 21331625
|
||||
chr12 49427651 49427652
|
||||
chr12 49444544 49444545
|
||||
chr12 121416621 121416622
|
||||
chr12 133202214 133202215
|
||||
chr13 21562947 21562948
|
||||
chr13 28609824 28609825
|
||||
chr13 32936645 32936646
|
||||
chr13 113889473 113889474
|
||||
chr13 113907390 113907391
|
||||
chr14 105239893 105239894
|
||||
chr14 105246324 105246325
|
||||
chr14 38064214 38064215
|
||||
chr14 20820536 20820537
|
||||
chr14 35871216 35871217
|
||||
chr15 41865487 41865488
|
||||
chr15 51502985 51502986
|
||||
chr15 51529111 51529112
|
||||
chr15 99456252 99456253
|
||||
chr15 99478224 99478225
|
||||
chr15 51558730 51558731
|
||||
chr16 68857440 68857441
|
||||
chr16 359952 359953
|
||||
chr16 89805976 89805977
|
||||
chr16 89838077 89838078
|
||||
chr16 89857963 89857964
|
||||
chr17 7983968 7983969
|
||||
chr17 29486151 29486152
|
||||
chr17 29508774 29508775
|
||||
chr17 29546174 29546175
|
||||
chr17 29559931 29559932
|
||||
chr17 29653292 29653293
|
||||
chr17 37879761 37879762
|
||||
chr17 62007497 62007498
|
||||
chr17 78919557 78919558
|
||||
chr19 3110348 3110349
|
||||
chr19 3119238 3119239
|
||||
chr19 4101061 4101062
|
||||
chr19 11136214 11136215
|
||||
chr19 15289612 15289613
|
||||
chr19 15295133 15295134
|
||||
chr19 41725270 41725271
|
||||
chr20 43956526 43956527
|
||||
chr20 43956635 43956636
|
||||
chr20 43958849 43958850
|
||||
chr20 43958871 43958872
|
||||
chr20 54959295 54959296
|
||||
chr20 54961540 54961541
|
||||
chr21 37518705 37518706
|
||||
chr21 39752672 39752673
|
||||
chr21 39753374 39753375
|
||||
chr22 41568479 41568480
|
||||
chr22 30038151 30038152
|
||||
chr22 30079212 30079213
|
||||
chrX 76937962 76937963
|
||||
chrX 39922358 39922359
|
||||
chrX 39932906 39932907
|
||||
chrX 44938562 44938563
|
||||
chrX 100608190 100608191
|
||||
chrX 100611284 100611285
|
||||
chrX 76940533 76940534
|
||||
chr1 2488152 2488153
|
||||
chr1 23885598 23885599
|
||||
chr1 65321387 65321388
|
||||
chr1 120612005 120612006
|
||||
chr1 193094374 193094375
|
||||
chr1 226570839 226570840
|
||||
chr2 47693958 47693959
|
||||
chr2 48030837 48030838
|
||||
chr2 61749715 61749716
|
||||
chr2 141032087 141032088
|
||||
chr2 215645463 215645464
|
||||
chr3 30686413 30686414
|
||||
chr3 47125384 47125385
|
||||
chr3 134644635 134644636
|
||||
chr3 142281611 142281612
|
||||
chr3 192053273 192053274
|
||||
chr4 55599435 55599436
|
||||
chr4 143007418 143007419
|
||||
chr4 153252060 153252061
|
||||
chr4 185310217 185310218
|
||||
chr4 25666098 25666099
|
||||
chr5 35857176 35857177
|
||||
chr5 38955795 38955796
|
||||
chr5 39074295 39074296
|
||||
chr5 67522721 67522722
|
||||
chr5 112162853 112162854
|
||||
chr5 149435758 149435759
|
||||
chr5 161119124 161119125
|
||||
chr5 170819886 170819887
|
||||
chr5 180046343 180046344
|
||||
chr6 30858856 30858857
|
||||
chr6 32797875 32797876
|
||||
chr6 36645695 36645696
|
||||
chr6 117678082 117678083
|
||||
chr6 117714345 117714346
|
||||
chr7 2946460 2946461
|
||||
chr7 2962752 2962753
|
||||
chr7 87138644 87138645
|
||||
chr7 151970930 151970931
|
||||
chr8 90955623 90955624
|
||||
chr8 90970934 90970935
|
||||
chr8 90995018 90995019
|
||||
chr8 68864727 68864728
|
||||
chr8 38322345 38322346
|
||||
chr8 145742878 145742879
|
||||
chr9 5081779 5081780
|
||||
chr9 8389363 8389364
|
||||
chr9 93657760 93657761
|
||||
chr9 98209593 98209594
|
||||
chr9 21991922 21991923
|
||||
chr9 37020621 37020622
|
||||
chr9 21975016 21975017
|
||||
chr10 43600688 43600689
|
||||
chr10 89720906 89720907
|
||||
chr10 104596980 104596981
|
||||
chr10 104849467 104849468
|
||||
chr10 104855655 104855656
|
||||
chr10 123239111 123239112
|
||||
chr11 32410773 32410774
|
||||
chr11 69462909 69462910
|
||||
chr11 94197259 94197260
|
||||
chr11 94225806 94225807
|
||||
chr11 94225919 94225920
|
||||
chr11 125497465 125497466
|
||||
chr12 1040372 1040373
|
||||
chr12 4553382 4553383
|
||||
chr12 6711146 6711147
|
||||
chr12 21331624 21331625
|
||||
chr12 49427651 49427652
|
||||
chr12 49444544 49444545
|
||||
chr12 121416621 121416622
|
||||
chr12 133202214 133202215
|
||||
chr13 21562947 21562948
|
||||
chr13 28609824 28609825
|
||||
chr13 32936645 32936646
|
||||
chr13 113889473 113889474
|
||||
chr13 113907390 113907391
|
||||
chr14 105239893 105239894
|
||||
chr14 105246324 105246325
|
||||
chr14 38064214 38064215
|
||||
chr14 20820536 20820537
|
||||
chr14 35871216 35871217
|
||||
chr15 41865487 41865488
|
||||
chr15 51502985 51502986
|
||||
chr15 51529111 51529112
|
||||
chr15 99456252 99456253
|
||||
chr15 99478224 99478225
|
||||
chr15 51558730 51558731
|
||||
chr16 68857440 68857441
|
||||
chr16 359952 359953
|
||||
chr16 89805976 89805977
|
||||
chr16 89838077 89838078
|
||||
chr16 89857963 89857964
|
||||
chr17 7983968 7983969
|
||||
chr17 29486151 29486152
|
||||
chr17 29508774 29508775
|
||||
chr17 29546174 29546175
|
||||
chr17 29559931 29559932
|
||||
chr17 29653292 29653293
|
||||
chr17 37879761 37879762
|
||||
chr17 62007497 62007498
|
||||
chr17 78919557 78919558
|
||||
chr19 3110348 3110349
|
||||
chr19 3119238 3119239
|
||||
chr19 4101061 4101062
|
||||
chr19 11136214 11136215
|
||||
chr19 15289612 15289613
|
||||
chr19 15295133 15295134
|
||||
chr19 41725270 41725271
|
||||
chr20 43956526 43956527
|
||||
chr20 43956635 43956636
|
||||
chr20 43958849 43958850
|
||||
chr20 43958871 43958872
|
||||
chr20 54959295 54959296
|
||||
chr20 54961540 54961541
|
||||
chr21 37518705 37518706
|
||||
chr21 39752672 39752673
|
||||
chr21 39753374 39753375
|
||||
chr22 41568479 41568480
|
||||
chr22 30038151 30038152
|
||||
chr22 30079212 30079213
|
||||
chrX 39932906 39932907
|
||||
chrX 44938562 44938563
|
||||
chrX 76937962 76937963
|
||||
chrX 76940533 76940534
|
||||
chrX 100608190 100608191
|
||||
chrX 100611284 100611285
|
||||
chrX 44833840 44833841
|
||||
chrX 53228147 53228148
|
||||
chrX 44929076 44929077
|
||||
chrX 47424614 47424615
|
||||
|
|
|
|||
|
|
@ -1,11 +1,11 @@
|
|||
#chr start end rs
|
||||
chrX 39922358 39922359 rs3810694
|
||||
chrX 39932906 39932907 rs6520618
|
||||
chrX 44833840 44833841 rs6611055
|
||||
chrX 76937962 76937963 rs3088074
|
||||
chrX 76940533 76940534 rs35268552
|
||||
chrX 100608190 100608191 rs1135363
|
||||
chrX 100611284 100611285 rs3747288
|
||||
chrX 53228147 53228148 rs1977364
|
||||
chrX 44929076 44929077 rs2230018
|
||||
chrX 47424614 47424615 rs2071776
|
||||
#chr start end rs
|
||||
chrX 39932906 39932907 rs6520618
|
||||
chrX 44938562 44938563 rs20539
|
||||
chrX 76937962 76937963 rs3088074
|
||||
chrX 76940533 76940534 rs35268552
|
||||
chrX 100608190 100608191 rs1135363
|
||||
chrX 100611284 100611285 rs3747288
|
||||
chrX 44833840 44833841 rs6611055
|
||||
chrX 53228147 53228148 rs1977364
|
||||
chrX 44929076 44929077 rs2230018
|
||||
chrX 47424614 47424615 rs2071776
|
||||
|
|
|
|||
|
|
@ -98,46 +98,24 @@ open POS, ">$output.pos.txt";
|
|||
my $h2 = <IN>;
|
||||
chomp $h2;
|
||||
|
||||
print POS $h2 . "\tOncogenic\t" . join("\t", (split("\t", $h1))[0 .. 9, 14]) . "\tLabel\tDrugCn\tIndication\n";
|
||||
print POS $h2 . "\t" . join("\t", (split("\t", $h1))[0 .. 9, 14]) . "\tLabel\tDrugCn\tIndication\n";
|
||||
|
||||
my @pos;
|
||||
while (<IN>) {
|
||||
chomp;
|
||||
my @splitline = split(/\t/);
|
||||
|
||||
my $freq = (split(/:/, $splitline[9]))[9] / (split(/:/, $splitline[9]))[7];
|
||||
|
||||
if (exists $therapy{lc 'BCL2L11'}{lc 'DELETION POLYMORPHISM'}) {
|
||||
print "$freq\n";
|
||||
foreach my $entry (@{$therapy{lc 'BCL2L11'}{lc 'DELETION POLYMORPHISM'}}) {
|
||||
|
||||
my @line = split("\t", $entry);
|
||||
if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
|
||||
# push @pos, "$_\t.\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
push @pos, "$_\t.\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
}
|
||||
elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
|
||||
# push @pos, "$_\t.\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
push @pos, "$_\t.\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
}
|
||||
elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
|
||||
# push @pos, "$_\t.\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
push @pos, "$_\t.\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
push @pos, "$_\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
}
|
||||
|
||||
# my @line = split("\t", $entry);
|
||||
# if (($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and $line[2] =~ /$cancer_type|solid tumor/i) {
|
||||
# push @pos, "$_\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
# }
|
||||
# elsif (($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and $line[2] !~ /$cancer_type|solid tumor/i) {
|
||||
# push @pos, "$_\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
# }
|
||||
# elsif ($line[2] =~ /$cancer_type|solid tumor/i) {
|
||||
# push @pos, "$_\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
|
||||
# }
|
||||
# else {
|
||||
# print "未匹配到"
|
||||
# }
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue