scripts/utilities/bp_download_query_genbank.pl

   1 #!/usr/bin/perl
   2
   3
   4 =head1 NAME
   5
   6 bp_download_query_genbank - script to query Genbank and retrieve records
   7
   8 =head1 USAGE
   9
  10  bp_download_query_genbank --query "Neurospora[ORGN]" --db nucest -o Ncrassa_ESTs.fa --format fasta
  11
  12  bp_download_query_genbank --queryfile 'filewithquery' --db nucest -o Ncrassa_ESTs.fa --format fasta
  13
  14 =head2 Other options
  15
  16  Provide ONE of:
  17
  18   -q --query query string OR
  19   --queryfile profile file with query OR
  20   --gi --gis --gifile file with list of GIs to download
  21
  22  Database type:
  23
  24  -d --db database (nucleotide [default], nucest, protein, )
  25
  26  -o --out --outfile output file (results are displayed on screen otherwise)
  27  -f --format sequence file output format (fasta by default)
  28  -v --verbose debugging output
  29
  30 =head2 Query options
  31
  32  --maxids maximum number of IDs to retrieve in a set (100 at a time by default)
  33  --reldate
  34  --maxdate maxdate for a record
  35  --mindate minimum date for record
  36  --datetype edat or mdat (entered or modified)
  37
  38 =head1 AUTHOR Jason Stajich
  39
  40 Jason Stajich, jason-AT-bioperl.org
  41
  42 =cut
  43
  44 use strict;
  45 use warnings;
  46 use Bio::DB::GenBank;
  47 use Bio::DB::GenPept;
  48 use Bio::DB::Query::GenBank;
  49 use Bio::SeqIO;
  50 use Getopt::Long;
  51
  52 my ($queryfile,$outfile,$format,$debug,%options);
  53
  54 $format = 'fasta';
  55
  56 $options{'-maxids'} = '100';
  57 $options{'-db'} = 'nucleotide'; # can be nucleotide, nucest, protein
  58 my $gifile;
  59 GetOptions(
  60                    'h|help' => sub { exec('perldoc', $0);
  61                                                                         exit(0);
  62                                                                 },
  63                           'v|verbose'       => \$debug,
  64                           'f|format:s'      => \$format,
  65                           'queryfile:s'     => \$queryfile,
  66                           'o|out|outfile:s' => \$outfile,
  67                           'gi|gifile|gis:s' => \$gifile,
  68                           # DB::Query options
  69                           'd|db:s'     => \$options{'-db'},
  70                           'mindate:s'  => \$options{'-mindate'},
  71                           'maxdate:s'  => \$options{'-maxdate'},
  72                           'reldate:s'  => \$options{'-reldate'},
  73                           'datetype:s' => \$options{'-datetype'}, # edat or mdat
  74                           'maxids:i'   => \$options{'-maxids'},
  75                           'q|query:s'  => \$options{'-query'},
  76                          );
  77
  78 my $out;
  79
  80 if( $outfile ) {
  81         $out = Bio::SeqIO->new(-format => $format,
  82                                                                   -file   => ">$outfile");
  83 } else {
  84         $out = Bio::SeqIO->new(-format => $format); # write to STDOUT
  85 }
  86
  87 my $dbh;
  88 if( $options{'-db'} eq 'protein' ) {
  89         $dbh = Bio::DB::GenPept->new(-verbose => $debug);
  90 } else {
  91         $dbh = Bio::DB::GenBank->new(-verbose => $debug);
  92 }
  93 my $query;
  94 if( $gifile ) {
  95         my @ids;
  96         open my $fh, '<', $gifile or die "Could not read file '$gifile': $!\n";
  97         while(<$fh>) {
  98                 push @ids, split;
  99         }
 100         close $fh;
 101         while( @ids ) {
 102                 my @mini_ids = splice(@ids, 0, $options{'-maxids'});
 103                 $query = Bio::DB::Query::GenBank->new(%options,
 104                                                       -verbose =>$debug,
 105                                                       -ids => \@mini_ids,
 106                                                      );
 107                 my $stream = $dbh->get_Stream_by_query($query);
 108                 while( my $seq = $stream->next_seq ) {
 109                         $out->write_seq($seq);
 110                 }
 111         }
 112         exit;
 113 } elsif( $options{'-query'}) {
 114         $query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
 115 } elsif( $queryfile ) {
 116         open my $fh, '<', $queryfile or die "Could not read file '$queryfile': $!\n";
 117         while(<$fh>) {
 118                 chomp;
 119                 $options{'-query'} .= $_;
 120         }
 121         $query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
 122         close $fh;
 123 } else {
 124         die("no query string or gifile\n");
 125 }
 126 my $stream = $dbh->get_Stream_by_query($query);
 127 while( my $seq = $stream->next_seq ) {
 128         $out->write_seq($seq);
 129 }