scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS

   1 #!/usr/bin/env perl
   2 # AUTHOR: malcolm.cook@stowers-institute.org
   3
   4 use strict;
   5
   6 use Carp;
   7 use Getopt::Long;
   8 use File::Spec;
   9 use Bio::DB::SeqFeature::Store;
  10
  11 #use Carp::Always;
  12
  13 my $DSN;
  14 my $ADAPTOR;
  15 my $VERBOSE  = 1;
  16 my $USER     = '';
  17 my $PASS     = '';
  18 my @gff3opt;
  19
  20 GetOptions(
  21            'dsn=s'       => \$DSN,
  22            'adaptor=s'   => \$ADAPTOR,
  23            'user=s'      => \$USER,
  24            'password=s'  => \$PASS,
  25            'gff3opt=i{,}'    => \@gff3opt,
  26           ) || die <<END;
  27 Usage: $0 [options] -- [WHICH FEATURES]
  28   output GFF3 for selected database features
  29   Options:
  30           -d --dsn        The database name ($DSN)
  31           -a --adaptor    The storage adaptor to use ($ADAPTOR)
  32           -u --user       User to connect to database as
  33           -p --password   Password to use to connect to database
  34           -g --gff3opt    flag options to gff3_string (i.e.: pass -gffopt 1 to recurse)
  35
  36          WHICH FEATURES: any remaining options after '--' will select
  37          a subset of features. The arguments are identical to those
  38          accepted by Bio::DB::SeqFeature::Store->features().
  39
  40 END
  41
  42 $ADAPTOR     ||= 'DBI::mysql';
  43 $DSN         ||= $ADAPTOR eq 'DBI::mysql' ? "mysql_read_default_file=$ENV{HOME}/.my.cnf" : '';
  44
  45 my $store = Bio::DB::SeqFeature::Store->new(
  46                                             -dsn     => $DSN,
  47                                             -adaptor => $ADAPTOR,
  48                                             -user    => $USER,
  49                                             -pass    => $PASS,
  50                                            )
  51   or die "Couldn't create connection to the database";
  52
  53 # on signals, give objects a chance to call their DESTROY methods
  54 $SIG{TERM} = $SIG{INT} = sub {   undef $store; die "Aborted..."; };
  55
  56 my $seq_stream = $store->get_seq_stream(@ARGV)  or die "failed to get_seq_stream(@ARGV)";
  57 while (my $seq = $seq_stream->next_seq) {
  58   ### 20100725 // genehack
  59   # Try to call a gff3_string() method, but fall back to gff_string() if $seq
  60   # doesn't support that. Note that gff_string() is required per
  61   # Bio::SeqFeatureI, while gff3_string() is not. Currently, only
  62   # Bio::SeqFeature::Lite implements gff3_string().
  63   if ( $seq->can( 'gff3_string' )) {
  64     print $seq->gff3_string(@gff3opt) . "\n";
  65   }
  66   elsif ( $seq->can( 'gff_string' )) {
  67     # since we intend on getting a GFF3 string, make sure to pass the version
  68     $seq->gff_format->gff_version(3);
  69     print $seq->gff_string() . "\n";
  70   }
  71   else {
  72     confess "sequence object $seq does not support gff3_string() or gff_string() methods!"
  73   }
  74 }
  75
  76 exit 0;