examples/cluster/dbsnp.pl

   1 #!/usr/bin/perl
   2
   3 # allenday@ucla.edu
   4 # parses a dbsnp xml file, prints some info for each refsnp and subsnp
   5
   6 use strict;
   7 use Bio::ClusterIO;
   8 use Bio::Root::IO;
   9 use IO::File;
  10
  11 my $file = shift @ARGV;
  12
  13 my $io = Bio::ClusterIO->new    (       -tempfile => 0,
  14                                         -format   => 'dbsnp',
  15                                         -fh       => IO::File->new("zcat $file |"),
  16                                 );
  17
  18 while(my $cluster = $io->next_cluster){
  19         print $cluster->id,"\t", $cluster->observed, "\n";
  20
  21         foreach my $subsnp ($cluster->each_subsnp){
  22                 print "\t\t\t", $subsnp->id, "\t", $subsnp->handle, "\t", $subsnp->method, "\n";
  23
  24         }
  25 }