perl/etc/justonce/checkrange.pl

   1 #!/usr/bin/env perl
   2
   3 use strict;
   4 use warnings;
   5
   6 use Data::Dump qw(ddx);
   7
   8 my %STRs;
   9 while (my $data_string = <DATA>) {
  10         chomp($data_string);
  11         next if not length $data_string;
  12         next if $data_string =~ /^#/;
  13         #print "[$data_string]\n";
  14         my @item = split /\t/,$data_string;
  15         $STRs{$item[1]} = [$item[3],$item[4]];
  16 }
  17 ddx \%STRs;
  18
  19 # bcftools query -f '%CHROM\t%POS\t%ID\t%REF,%ALT[\t%TGT]\n' ALL.chrY.phase3_integrated_v2a.20130502.genotypes.vcf.gz|less -S
  20
  21 while (<>) {
  22         chomp;
  23         my ($chr,$pos,$id) = split /\t/;
  24         #print "$chr,$pos,$id\n";
  25         next if $chr ne 'Y';
  26         for my $k (sort keys %STRs) {
  27                 my ($st,$ed) = @{$STRs{$k}};
  28                 #print "$st,$ed $pos\n";
  29                 if (($st <= $pos+200) and ($ed >= $pos-200)) {
  30                         print join("\t",$k,$st,$ed,$chr,$pos,$id),"\n";
  31                 }
  32         }
  33 }
  34 __DATA__
  35 #Tag    ID      Chr     Start   End
  36 Y-STR   AMEL    Y       6868712 6868744
  37 Y-STR   DYF387S1a       Y       23785361        23785500
  38 Y-STR   DYF387S1b       Y       25884581        25884724
  39 Y-STR   DYF404S1a       Y       23807934        23808051
  40 Y-STR   DYF404S1b       Y       25862038        25862147
  41 Y-STR   DYS19   Y       9684380 9684443
  42 Y-STR   DYS385a Y       18639713        18639756
  43 Y-STR   DYS385b Y       18680632        18680687
  44 Y-STR   DYS388  Y       12635604        12635639
  45 Y-STR   DYS389I Y       12500448        12500495
  46 Y-STR   DYS389II        Y       12500448        12500611
  47 Y-STR   DYS390  Y       15163067        15163162
  48 Y-STR   DYS391  Y       11982089        11982132
  49 Y-STR   DYS392  Y       20471987        20472025
  50 Y-STR   DYS393  Y       3263111 3263158
  51 Y-STR   DYS437  Y       12346267        12346326
  52 Y-STR   DYS438  Y       12825889        12825948
  53 Y-STR   DYS439  Y       12403517        12403564
  54 Y-STR   DYS444  Y       17114310        17114365
  55 Y-STR   DYS447  Y       13166829        13166953
  56 Y-STR   DYS448  Y       22218923        22219078
  57 Y-STR   DYS449  Y       8349973 8350138
  58 Y-STR   DYS456  Y       4402919 4402978
  59 Y-STR   DYS458  Y       7999839 7999902
  60 Y-STR   DYS459a Y       23932704        23932743
  61 Y-STR   DYS459b Y       25737373        25737408
  62 Y-STR   DYS460  Y       18888956        18888995
  63 Y-STR   DYS481  Y       8558337 8558402
  64 Y-STR   DYS510  Y       15188001        15188088
  65 Y-STR   DYS518  Y       15207988        15208145
  66 Y-STR   DYS522  Y       7547585 7547624
  67 Y-STR   DYS527a Y       23739650        23739733
  68 Y-STR   DYS527b Y       25930351        25930426
  69 Y-STR   DYS531  Y       8598154 8598197
  70 Y-STR   DYS533  Y       16281349        16281396
  71 Y-STR   DYS549  Y       19358338        19358389
  72 Y-STR   DYS557  Y       21072786        21072889
  73 Y-STR   DYS570  Y       6993190 6993257
  74 Y-STR   DYS576  Y       7185318 7185385
  75 Y-STR   DYS593  Y       16473882        16473956
  76 Y-STR   DYS596  Y       8519499 8519594
  77 Y-STR   DYS627  Y       8781984 8782055
  78 Y-STR   DYS635  Y       12258860        12258951
  79 Y-STR   DYS643  Y       15314132        15314186
  80 Y-STR   DYS645  Y       21166023        21166057
  81 Y-STR   YGATAA10        Y       16607009        16607060
  82 Y-STR   YGATAH4 Y       16631673        16631720
  83 Y-STR   Yindel  Y       13396821        13396825