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# $Id: bp_genbank2gff.PLS,v 1.14 2004/05/05 13:37:12 scain Exp $
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bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.
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% bp_genbank2gff.pl -d genbank -f localfile.gb
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% bp_genbank2gff.pl -d genbank --accession AP003256
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% bp_genbank2gff.pl --accession AP003256 --stdout
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This script loads a Bio::DB::GFF database with the features contained
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in a either a local genbank file or an accession that is fetched from
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genbank. Various command-line options allow you to control which
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database to load and whether to allow an existing database to be
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The database must already have been created and the current user must
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have appropriate INSERT and UPDATE privileges. The --create option
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will initialize a new database with the appropriate schema, deleting
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any tables that were already there.
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=head1 COMMAND-LINE OPTIONS
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Command-line options can be abbreviated to single-letter options.
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e.g. -d instead of --database.
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--create Force creation and initialization of database
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--dsn <dsn> Data source (default dbi:mysql:test)
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--user <user> Username for mysql authentication
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--pass <password> Password for mysql authentication
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--proxy <proxy> Proxy server to use for remote access
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--stdout direct output to STDOUT
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--adaptor <adaptor> adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle) --viral the genome you are loading is viral (changes tag
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--source <source> source field for features ['genbank']
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EITHER --file Arguments that follow are Genbank/EMBL file names
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OR --gb_folder What follows is a folder full of gb files to process OR --accession Arguments that follow are genbank accession numbers
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OR --acc_file Accession numbers (not gi!) in a file (one per line, no punc.)
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OR --acc_pipe Accession numbers (not gi!) from a STDIN pipe (one
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L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
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Scott Cain, cain@cshl.org
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Copyright (c) 2003 Cold Spring Harbor Laboratory
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This library is free software; you can redistribute it and/or modify
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it under the same terms as Perl itself. See DISCLAIMER.txt for
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disclaimers of warranty.
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package Bio::DB::GFF::Adaptor::biofetch_to_stdout;
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use Bio::DB::GFF::Util::Rearrange;
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use Bio::DB::GFF::Adaptor::biofetch;
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@ISA = 'Bio::DB::GFF::Adaptor::biofetch';
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my ($self,$options) = @_;
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# synthesize GFF3-compatible line
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if (my $id = $options->{gname}) {
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$parent =~ s/\..\d+$// if $options->{method} =~ /^(mRNA|transcript|exon|gene)$/;
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push @attributes,"Parent=".escape($parent) if $options->{method} =~ /^(variation|exon|CDS|transcript|mRNA|coding)$/;
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push @attributes,"ID=".escape($id) unless $options->{method} =~ /^(exon|CDS)$/;
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if (my $tstart = $options->{tstart}) {
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my $tstop = $options->{tstop};
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my $target = escape($options->{gname});
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push @attributes,"Target=$target+$tstart+$tstop";
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if (my $attributes = $options->{attributes}) {
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for my $a (@$attributes) {
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my ($tag,$value) = @$a;
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push @{$a{escape($tag)}},escape($value);
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push @attributes,"$a=".join(',',@{$a{$a}});
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${$options}{'score'} = "." unless ${$options}{'score'};
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${$options}{'strand'} = "." unless ${$options}{'strand'};
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${$options}{'phase'} = "." unless ${$options}{'phase'};
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my $last_column = join ';',@attributes;
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if ($options->{method} eq 'origin') {
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print "##sequence-region $options->{gname} $options->{start} $options->{stop}\n";
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print join("\t",@{$options}{qw(ref source method start stop score strand phase)},$last_column),"\n";
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sub load_sequence_string {
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$seq =~ s/(.{1,60})/$1\n/g;
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print ">$acc\n\L$seq\U\n";
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print "##gff-version 3\n";
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Usage: $0 [options] [<gff file 1> <gff file 2>] ...
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Load a Bio::DB::GFF database from GFF files.
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--create Force creation and initialization of database
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--dsn <dsn> Data source (default dbi:mysql:test)
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--user <user> Username for mysql authentication
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--pass <password> Password for mysql authentication
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--proxy <proxy> Proxy server to use for remote access
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--stdout direct output to STDOUT
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--adaptor <adaptor> adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle)
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--viral the genome you are loading is viral (changes tag
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--source <source> source field for features ['genbank']
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EITHER --file Arguments that follow are Genbank/EMBL file names
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OR --gb_folder What follows is a folder full of gb files to process
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OR --accession Arguments that follow are genbank accession numbers
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OR --acc_file Accession numbers (not gi!) in a file (one per line,
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OR --acc_pipe Accession numbers (not gi!) from a STDIN pipe (one
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This script loads a Bio::DB::GFF database with the features contained
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in a either a local genbank file or an accession that is fetched from
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genbank. Various command-line options allow you to control which
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database to load and whether to allow an existing database to be
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my ($DSN,$ADAPTOR,$CREATE,$USER,$VIRAL,$PASSWORD,$gbFOLDER,
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$FASTA,$ACC,$accFILE, $accPIPE, $FILE,$PROXY,$STDOUT,$SOURCE);
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'password:s' => \$PASSWORD,
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'adaptor:s' => \$ADAPTOR,
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'accession' => \$ACC,
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'acc_file' => \$accFILE,
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'acc_pipe' => \$accPIPE,
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'source:s' => \$SOURCE,
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'gb_folder=s' => \$gbFOLDER,
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'proxy:s' => \$PROXY,
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'stdout' => \$STDOUT,
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'create' => \$CREATE) or die $USAGE;
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die $USAGE unless ($DSN || $STDOUT); # at a minimum we need to have a place to write to!
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# some local defaults
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$DSN ||= 'dbi:mysql:test';
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$ADAPTOR ||= $STDOUT ? 'memory' : 'dbi::mysql';
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# Ensure that biofetch inherits from the "right" adaptor.
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# This is a horrible hack and should be fixed.
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eval "use Bio::DB::GFF::Adaptor::${ADAPTOR}";
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local @Bio::DB::GFF::Adaptor::biofetch::ISA = "Bio::DB::GFF::Adaptor::${ADAPTOR}";
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my $biofetch = $STDOUT ? 'biofetch_to_stdout' : 'biofetch';
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my @dsn = $STDOUT ? () : (-dsn => $DSN);
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push @auth,(-user=>$USER) if defined $USER;
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push @auth,(-pass=>$PASSWORD) if defined $PASSWORD;
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push @auth,(-proxy=>$PROXY) if defined $PROXY;
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my %preferred_tags = (
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$preferred_tags{'product'} = 90 if $VIRAL; # added this to the default list for viral genomes
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# since most functions come from post-translational processing, so the default labels are c**p!
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my $db = Bio::DB::GFF->new(-adaptor=>$biofetch,
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-preferred_tags => \%preferred_tags,
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-source=> $SOURCE || 'Genbank')
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or die "Can't open database: ",Bio::DB::GFF->error,"\n";
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die "you must specify either an accession to retrieve from\nembl or a local file containing data in embl format\n" if (($FILE || $ACC) && !scalar(@ARGV));
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status(loading => $_);
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my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
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status(done => $result);
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status('loading' => $_);
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my $result = $db->load_from_file($_);
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status (done => $result);
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my $filename = shift;
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die "you must supply a filename after the --accFILE command line flag\n" unless $filename;
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die "file $filename does not exist\n" unless (-e $filename && !(-d $filename));
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open IN, "$filename" || die "Can't open file $filename for reading accession numbers: $!\n";
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status(loading => $_);
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my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
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status(done => $result);
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die "folder $dir does not exist\n" unless (-e $dir && -d $dir);
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opendir DIR, "$dir" || die "can't open directory $dir for reading: $!\n";
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my @files = readdir DIR;
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foreach my $file(@files){
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if (!(-e "$gbFOLDER/$file") || (-d "$gbFOLDER/$file")){
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print STDERR " $gbFOLDER/$file is not a filename! Skipping...\n";
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my $result = $db->load_from_file("$gbFOLDER/$file");
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print STDERR $result ? "ok\n" : "failed\n";
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my @accessions = <STDIN>;
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foreach (@accessions){
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status(loading => $_);
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my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
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status(done => $result);
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status(loading => $_);
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my $result = $db->load_from_file($_);
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status(done => $result);
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$done || die "\n\nno source of data provided\n\n";
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my ($state,$msg) = @_;
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if ($state eq 'loading') {
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print STDERR "Loading $msg...";
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} elsif ($state eq 'done') {
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print STDERR $msg ? "ok\n" : "failed\n";
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scripts/Bio-DB-GFF/bp_genbank2gff.PLS
