scripts/biosql/bioentry2flat.pl

   1 #!/usr/local/bin/perl
   2
   3 use Bio::DB::BioDB;
   4 use Bio::Seq::RichSeq;
   5 use Bio::SeqIO;
   6 use Getopt::Long;
   7
   8 my $outfmt = 'EMBL';
   9 my $host = undef;
  10 my $sqlname = "bioperl_db";
  11 my $dbuser = "root";
  12 my $dbpass = undef;
  13 my $dbname = '';
  14 my $acc;
  15 my $version;
  16 my $stdout=0;
  17 my $format='embl';
  18 my $file;
  19 my $driver = 'mysql';
  20
  21 &GetOptions( 'host=s' => \$host,
  22              'driver=s' => \$driver,
  23              'dbuser=s' => \$dbuser,
  24              'dbpass=s' => \$dbpass,
  25              'dbname=s' => \$dbname,
  26              'accession=s' => \$acc,
  27              'version=s' => \$version,
  28              'format:s' => \$format,
  29              'outformat:s' => \$outfmt,
  30              'file:s' => \$file
  31              );
  32
  33 $biodbname = 'sprot_hum';
  34
  35 $dbname = shift @ARGV unless $dbname;
  36 $acc    = shift @ARGV unless $acc;
  37
  38 #
  39 # create the DBAdaptorI for our database
  40 #
  41 print STDERR "Connecting with $driver:$dbname:$dbuser:dbpass\n";
  42
  43 my $db = Bio::DB::BioDB->new(-database => "biosql",
  44                              -host     => $host,
  45                              -dbname   => $dbname,
  46                              -driver   => $driver,
  47                              -user     => $dbuser,
  48                              -pass     => $dbpass,
  49                              );
  50
  51
  52 my $seqadaptor = $db->get_object_adaptor('Bio::SeqI');
  53
  54 my $seq = Bio::Seq::RichSeq->new( -accession_number => $acc,
  55                                   -version => $version,
  56                                   -namespace => $biodbname );
  57
  58 $seq = $seqadaptor->find_by_unique_key($seq);
  59
  60 my $seqio;
  61
  62 if ($file) {
  63     print STDERR "Going the $file way...";
  64     $seqio = Bio::SeqIO->new('-format' => $format,-file => ">$file");
  65     $seqio->write_seq($seq);
  66 }
  67 else {
  68     $out = Bio::SeqIO->newFh('-format' => $outfmt);
  69     print $out $seq;
  70 }
  71
  72
  73
  74
  75