Bio::DB::SeqFeature::Store GFF3Loader
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Summary
Bio::DB::SeqFeature::Store::GFF3Loader -- GFF3 file loader for Bio::DB::SeqFeature::Store
Package variables
Privates (from "my" definitions)
%Strandedness = ( '+' => 1, '-' => -1, '.' => 0, '' => 0, 0 => 0, 1 => 1, -1 => -1, +1 => 1, undef => 0, )
%Special_attributes = ( Gap => 1, Target => 1, Parent => 1, Name => 1, Alias => 1, ID => 1, index => 1, Index => 1, )
Included modules
Bio::DB::GFF::Util::Rearrange
Bio::DB::SeqFeature::Store::LoadHelper
Carp ' croak '
Inherit
Bio::DB::SeqFeature::Store::Loader
Synopsis
  use Bio::DB::SeqFeature::Store;
use Bio::DB::SeqFeature::Store::GFF3Loader;
# Open the sequence database my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql', -dsn => 'dbi:mysql:test', -write => 1 ); my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store => $db, -verbose => 1, -fast => 1); $loader->load('./my_genome.gff3');
Description
The Bio::DB::SeqFeature::Store::GFF3Loader object parsers GFF3-format
sequence annotation files and loads Bio::DB::SeqFeature::Store
databases. For certain combinations of SeqFeature classes and
SeqFeature::Store databases it features a "fast load" mode which will
greatly accelerate the loading of GFF3 databases by a factor of 5-10.
The GFF3 file format has been extended very slightly to accommodate
Bio::DB::SeqFeature::Store. First, the loader recognizes is a new
directive:
  # #index-subfeatures [0|1]
Note that you can place a space between the two #'s in order to
prevent GFF3 validators from complaining.
If this is true, then subfeatures are indexed (the default) so that
they can be retrieved with a query. See Bio::DB::SeqFeature::Store
for an explanation of this. If false, then subfeatures can only be
accessed through their parent feature.
Second, the loader recognizes a new attribute tag called index, which
if present, controls indexing of the current feature. Example:
 ctg123	. TF_binding_site 1000 1012 . + . ID=tfbs00001;index=1
You can use this to turn indexing on and off, overriding the default
for a particular feature.
Note that the loader keeps a record -- in memory -- of each feature
that it has processed. If you find the loader running out of memory on
particularly large GFF3 files, please split the input file into
smaller pieces and do the load in steps.
Methods
newDescriptionCode
ignore_seqregionDescriptionCode
noalias_targetDescriptionCode
create_load_data
No description
Code
finish_load
No description
Code
load_line
No description
Code
handle_meta
No description
Code
handle_feature
No description
Code
invalid_gff
No description
Code
allow_whitespace
No description
Code
build_object_tree
No description
Code
build_object_tree_in_tables
No description
Code
build_object_tree_in_features
No description
Code
attach_children
No description
Code
fetch
No description
Code
add_segment
No description
Code
parse_attributes
No description
Code
_remap
No description
Code
_indexit
No description
Code
_local2global
No description
Code
local_ids
No description
Code
loaded_ids
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(@options)
Function: create a new parser
Returns : a Bio::DB::SeqFeature::Store::GFF3Loader gff3 parser and loader
Args : several - see below
Status : public
This method creates a new GFF3 loader and establishes its connection
with a Bio::DB::SeqFeature::Store database. Arguments are -name=>$value
pairs as described in this table:
 Name               Value
---- -----
-store A writable Bio::DB::SeqFeature::Store database handle. -seqfeature_class The name of the type of Bio::SeqFeatureI object to create and store in the database (Bio::DB::SeqFeature by default) -sf_class A shorter alias for -seqfeature_class -verbose Send progress information to standard error. -fast If true, activate fast loading (see below) -chunk_size Set the storage chunk size for nucleotide/protein sequences (default 2000 bytes) -tmp Indicate a temporary directory to use when loading non-normalized features. -ignore_seqregion Ignore ##sequence-region directives. The default is to create a feature corresponding to the directive. -noalias_target Don't create an Alias attribute for a target_id named in a Target attribute. The default is to create an Alias attribute containing the target_id found in a Target attribute.
When you call new(), a connection to a Bio::DB::SeqFeature::Store
database should already have been established and the database
initialized (if appropriate).
Some combinations of Bio::SeqFeatures and Bio::DB::SeqFeature::Store
databases support a fast loading mode. Currently the only reliable
implementation of fast loading is the combination of DBI::mysql with
Bio::DB::SeqFeature. The other important restriction on fast loading
is the requirement that a feature that contains subfeatures must occur
in the GFF3 file before any of its subfeatures. Otherwise the
subfeatures that occurred before the parent feature will not be
attached to the parent correctly. This restriction does not apply to
normal (slow) loading.
If you use an unnormalized feature class, such as
Bio::SeqFeature::Generic, then the loader needs to create a temporary
database in which to cache features until all their parts and subparts
have been seen. This temporary databases uses the "berkeleydb"
adaptor. The -tmp option specifies the directory in which that
database will be created. If not present, it defaults to the system
default tmp directory specified by File::Spec->tmpdir().
The -chunk_size option allows you to tune the representation of
DNA/Protein sequence in the Store database. By default, sequences are
split into 2000 base/residue chunks and then reassembled as
needed. This avoids the problem of pulling a whole chromosome into
memory in order to fetch a short subsequence from somewhere in the
middle. Depending on your usage patterns, you may wish to tune this
parameter using a chunk size that is larger or smaller than the
default.
ignore_seqregioncodeprevnextTop
  $ignore_it = $loader->ignore_seqregion([$new_flag])
Get or set the ignore_seqregion flag, which if true, will cause
GFF3 ##sequence-region directives to be ignored. The default behavior
is to create a feature corresponding to the region.
noalias_targetcodeprevnextTop
  $noalias_target = $loader->noalias_target([$new_flag])
Get or set the noalias_target flag, which if true, will disable the creation of
an Alias attribute for a target_id named in a Target attribute. The default is
to create an Alias attribute containing the target_id found in a Target
attribute.
Methods code
newdescriptionprevnextTop
sub new {
     my $class = shift;
    my $self  = $class->SUPER::new(@_);
    my ($ignore_seqregion) = rearrange(['IGNORE_SEQREGION'],@_);
    $self->ignore_seqregion($ignore_seqregion);
    my ($noalias_target) = rearrange(['NOALIAS_TARGET'],@_);
    $self->noalias_target($noalias_target);
    $self;
}
ignore_seqregiondescriptionprevnextTop
sub ignore_seqregion {
    my $self = shift;
    my $d    = $self->{ignore_seqregion};
    $self->{ignore_seqregion} = shift if @_;
    $d;
}
noalias_targetdescriptionprevnextTop
sub noalias_target {
    my $self = shift;
    my $d    = $self->{noalias_target};
    $self->{noalias_target} = shift if @_;
    $d;
}
create_load_datadescriptionprevnextTop
sub create_load_data {
 #overridden  my $self = shift;
$self->SUPER::create_load_data; $self->{load_data}{TemporaryID} = "GFFLoad0000000"; $self->{load_data}{IndexSubfeatures} = $self->index_subfeatures(); $self->{load_data}{mode} = 'gff'; $self->{load_data}{Helper} = Bio::DB::SeqFeature::Store::LoadHelper->new($self->{tmpdir});
}
finish_loaddescriptionprevnextTop
sub finish_load {
 #overridden  my $self  = shift;
$self->store_current_feature(); # during fast loading, we will have a feature left at the very end
$self->start_or_finish_sequence(); # finish any half-loaded sequences
$self->msg("Building object tree..."); my $start = $self->time(); $self->build_object_tree; $self->msg(sprintf "%5.2fs\n",$self->time()-$start); if ($self->fast) { $self->msg("Loading bulk data into database..."); $start = $self->time(); $self->store->finish_bulk_update; $self->msg(sprintf "%5.2fs\n",$self->time()-$start); } eval {$self->store->commit}; # don't delete load data so that caller can ask for the loaded IDs
# $self->delete_load_data;
}
load_linedescriptionprevnextTop
sub load_line {
 #overridden    my $self = shift;
my $line = shift; chomp($line); my $load_data = $self->{load_data}; $load_data->{line}++; return unless $line =~ /^\S/; # blank line
# if it has a tab in it or looks like a chrom.sizes file, switch to gff mode
$load_data->{mode} = 'gff' if $line =~ /\t/ or $line =~ /^\w+\s+\d+\s*$/; if ($line =~ /^\#\s?\#\s*(.+)/) { ## meta instruction
$load_data->{mode} = 'gff'; $self->handle_meta($1); } elsif ($line =~ /^\#/) { $load_data->{mode} = 'gff'; # just to be safe
return; # comment
} elsif ($line =~ /^>\s*(\S+)/) { # FASTA lines are coming
$load_data->{mode} = 'fasta'; $self->start_or_finish_sequence($1); } elsif ($load_data->{mode} eq 'fasta') { $self->load_sequence($line); } elsif ($load_data->{mode} eq 'gff') { $self->handle_feature($line); if (++$load_data->{count} % 1000 == 0) { my $now = $self->time(); my $nl = -t STDOUT && !$ENV{EMACS} ? "\r" : "\n"; local $^W = 0; # kill uninit variable warning
$self->msg(sprintf("%d features loaded in %5.2fs (%5.2fs/1000 features)...%s$nl", $load_data->{count},$now - $load_data->{start_time}, $now - $load_data->{millenium_time}, ' ' x 80 )); $load_data->{millenium_time} = $now; } } else { $self->throw("I don't know what to do with this line:\n$line"); }
}
handle_metadescriptionprevnextTop
sub handle_meta {
  my $self = shift;
  my $instruction = shift;

  if ( $instruction =~ /^#$/ ) {
    $self->store_current_feature() ;   # during fast loading, we will have a feature left at the very end
$self->start_or_finish_sequence(); # finish any half-loaded sequences
if ( $self->store->can('handle_resolution_meta') ) { $self->store->handle_resolution_meta($instruction); } return; } if ($instruction =~ /sequence-region\s+(.+)\s+(-?\d+)\s+(-?\d+)/i && !$self->ignore_seqregion()) { my($ref,$start,$end,$strand) = $self->_remap($1,$2,$3,+1); my $feature = $self->sfclass->new(-name => $ref, -seq_id => $ref, -start => $start, -end => $end, -strand => $strand, -primary_tag => 'region'); $self->store->store($feature); return; } if ($instruction =~/index-subfeatures\s+(\S+)/i) { $self->{load_data}{IndexSubfeatures} = $1; $self->store->index_subfeatures($1); return; } if ( $self->store->can('handle_unrecognized_meta') ) { $self->store->handle_unrecognized_meta($instruction); return; }
}
handle_featuredescriptionprevnextTop
sub handle_feature {
 #overridden  my $self     = shift;
my $gff_line = shift; my $ld = $self->{load_data}; my $allow_whitespace = $self->allow_whitespace; # special case for a chrom.sizes-style line
my @columns; if ($gff_line =~ /^(\w+)\s+(\d+)\s*$/) { @columns = ($1,undef,'chromosome',1,$2,undef,undef,undef,"Name=$1"); } else { $gff_line =~ s/\s+/\t/g if $allow_whitespace; @columns = map {$_ eq '.' ? undef : $_ } split /\t/,$gff_line; } $self->invalid_gff($gff_line) if @columns < 4; $self->invalid_gff($gff_line) if @columns > 9 && $allow_whitespace; { local $^W = 0; if (@columns > 9) { #oops, split too much due to whitespace
$columns[8] = join(' ',@columns[8..$#columns]); } } my ($refname,$source,$method,$start,$end,$score,$strand,$phase,$attributes) = @columns; $self->invalid_gff($gff_line) unless defined $refname; $self->invalid_gff($gff_line) unless !defined $start || $start =~ /^[\d.-]+$/; $self->invalid_gff($gff_line) unless !defined $end || $end =~ /^[\d.-]+$/; $self->invalid_gff($gff_line) unless defined $method; $strand = $Strandedness{$strand||0}; my ($reserved,$unreserved) = $attributes ? $self->parse_attributes($attributes) : (); my $name = ($reserved->{Name} && $reserved->{Name}[0]); my $has_loadid = defined $reserved->{ID}[0]; my $feature_id = defined $reserved->{ID}[0] ? $reserved->{ID}[0] : $ld->{TemporaryID}++; my @parent_ids = @{$reserved->{Parent}} if defined $reserved->{Parent}; my $index_it = $ld->{IndexSubfeatures}; if (exists $reserved->{Index} || exists $reserved->{index}) { $index_it = $reserved->{Index}[0] || $reserved->{index}[0]; } # Everything in the unreserved hash becomes an attribute, so we copy
# some attributes over
$unreserved->{Note} = $reserved->{Note} if exists $reserved->{Note}; $unreserved->{Alias} = $reserved->{Alias} if exists $reserved->{Alias}; $unreserved->{Target} = $reserved->{Target} if exists $reserved->{Target}; $unreserved->{Gap} = $reserved->{Gap} if exists $reserved->{Gap}; $unreserved->{load_id}= $reserved->{ID} if exists $reserved->{ID}; # mec@stowers-institute.org, wondering why not all attributes are
# carried forward, adds ID tag in particular service of
# round-tripping ID, which, though present in database as load_id
# attribute, was getting lost as itself
# $unreserved->{ID}= $reserved->{ID} if exists $reserved->{ID};
# TEMPORARY HACKS TO SIMPLIFY DEBUGGING
$feature_id = '' unless defined $feature_id; $name = '' unless defined $name; # prevent uninit variable warnings
# push @{$unreserved->{Alias}},$feature_id if $has_loadid && $feature_id ne $name;
$unreserved->{parent_id} =\@ parent_ids if @parent_ids; # POSSIBLY A PERMANENT HACK -- TARGETS BECOME ALIASES
# THIS IS TO ALLOW FOR TARGET-BASED LOOKUPS
if (exists $reserved->{Target} && !$self->{noalias_target}) { my %aliases = map {$_=>1} @{$unreserved->{Alias}}; for my $t (@{$reserved->{Target}}) { (my $tc = $t) =~ s/\s+.*$//; # get rid of coordinates
$name ||= $tc; push @{$unreserved->{Alias}},$tc unless $name eq $tc || $aliases{$tc}; } } ($refname,$start,$end,$strand) = $self->_remap($refname,$start,$end,$strand) or return; my @args = (-display_name => $name, -seq_id => $refname, -start => $start, -end => $end, -strand => $strand || 0, -score => $score, -phase => $phase, -primary_tag => $method || 'feature', -source => $source, -tag => $unreserved, -attributes => $unreserved, ); # Here's where we handle feature lines that have the same ID (multiple locations, not
# parent/child relationships)
my $old_feat; # Current feature is the same as the previous feature, which hasn't yet been loaded
if (defined $ld->{CurrentID} && $ld->{CurrentID} eq $feature_id) { $old_feat = $ld->{CurrentFeature}; } # Current feature is the same as a feature that was loaded earlier
elsif (defined(my $id = $self->{load_data}{Helper}->local2global($feature_id))) { $old_feat = $self->fetch($feature_id) or $self->warn(<<END); ID=$feature_id has been used more than once, but it cannot be found in the database. This can happen if you have specified fast loading, but features sharing the same ID are not contiguous in the GFF file. This will be loaded as a separate feature. Line $.: "$_" END } # contiguous feature, so add a segment
warn $old_feat if defined $old_feat and !ref $old_feat; if (defined $old_feat) { # set this to 1 to disable split-location behavior
if (0 && @parent_ids) { # If multiple features are held together by the same ID
$feature_id = $ld->{TemporaryID}++; # AND they have a Parent attribute, this causes an undesirable
} # additional layer of aggregation. Changing the ID fixes this.
elsif ( $old_feat->seq_id ne $refname || $old_feat->start != $start || $old_feat->end != $end # make sure endpoints are distinct
) { $self->add_segment($old_feat,$self->sfclass->new(@args)); return; } } # we get here if this is a new feature
# first of all, store the current feature if it is there
$self->store_current_feature() if defined $ld->{CurrentID}; # now create the new feature
# (index top-level features only if policy asks us to)
my $feature = $self->sfclass->new(@args); $feature->object_store($self->store) if $feature->can('object_store'); # for lazy table features
$ld->{CurrentFeature} = $feature; $ld->{CurrentID} = $feature_id; my $top_level = !@parent_ids; my $has_id = defined $reserved->{ID}[0]; $index_it ||= $top_level; my $helper = $ld->{Helper}; $helper->indexit($feature_id=>1) if $index_it; $helper->toplevel($feature_id=>1) if !$self->{fast} && $top_level; # need to track top level features
# remember parentage
for my $parent (@parent_ids) { $helper->add_children($parent=>$feature_id); }
}
invalid_gffdescriptionprevnextTop
sub invalid_gff {
    my $self = shift;
    my $line = shift;
    $self->throw("invalid GFF line at line $self->{load_data}{line}.\n".$line);
}
allow_whitespacedescriptionprevnextTop
sub allow_whitespace {
    my $self = shift;
    my $d    = $self->{allow_whitespace};
    $self->{allow_whitespace} = shift if @_;
    $d;
}
build_object_treedescriptionprevnextTop
sub build_object_tree {
  my $self = shift;
  $self->subfeatures_in_table ? $self->build_object_tree_in_tables : $self->build_object_tree_in_features;
}
build_object_tree_in_tablesdescriptionprevnextTop
sub build_object_tree_in_tables {
  my $self = shift;
  my $store  = $self->store;
  my $helper = $self->{load_data}{Helper};

  while (my ($load_id,$children) = $helper->each_family()) {

      my $parent_id = $helper->local2global($load_id);
      die $self->throw("$load_id doesn't have a primary id") 
	  unless defined $parent_id;

      my @children  = map {$helper->local2global($_)} @$children;
      # this updates the table that keeps track of parent/child relationships,
# but does not update the parent object -- so (start,end) had better be right!!!
$store->add_SeqFeature($parent_id,@children); }
}
build_object_tree_in_featuresdescriptionprevnextTop
sub build_object_tree_in_features {
  my $self  = shift;
  my $store      = $self->store;
  my $tmp        = $self->tmp_store;
  my $ld         = $self->{load_data};
  my $normalized = $self->subfeatures_normalized;

  my $helper     = $ld->{Helper};

  while (my $load_id = $helper->each_toplevel) {
    my $feature  = $self->fetch($load_id)
      or $self->throw("$load_id (id="
		      .$helper->local2global($load_id)
		      ." should have a database entry, but doesn't");
    $self->attach_children($store,$ld,$load_id,$feature);
    # Indexed objects are updated, not created anew
$feature->primary_id(undef) unless $helper->indexit($load_id); $store->store($feature); }
}
attach_childrendescriptionprevnextTop
sub attach_children {
  my $self = shift;
  my ($store,$ld,$load_id,$feature)  = @_;

  my $children   = $ld->{Helper}->children() or return;
  for my $child_id (@$children) {
      my $child = $self->fetch($child_id)
	  or $self->throw("$child_id should have a database entry, but doesn't");
      $self->attach_children($store,$ld,$child_id,$child);   # recursive call
$feature->add_SeqFeature($child); }
}
fetchdescriptionprevnextTop
sub fetch {
  my $self    = shift;
  my $load_id = shift;
  my $helper  = $self->{load_data}{Helper};
  my $id      = $helper->local2global($load_id);

  return
      ($self->subfeatures_normalized || $helper->indexit($load_id)
       ? $self->store->fetch($id)
       : $self->tmp_store->fetch($id)
      );
}
add_segmentdescriptionprevnextTop
sub add_segment {
  my $self = shift;
  my ($parent,$child) = @_;

  if ($parent->can('add_segment')) { # probably a lazy table feature
my $segment_count = $parent->can('denormalized_segment_count') ? $parent->denormalized_segment_count : $parent->can('denormalized_segments ') ? $parent->denormalized_segments : $parent->can('segments') ? $parent->segments : 0; unless ($segment_count) { # convert into a segmented object
my $segment; if ($parent->can('clone')) { $segment = $parent->clone; } else { my %clone = %$parent; $segment = bless\% clone,ref $parent; } delete $segment->{segments}; eval {$segment->object_store(undef) }; $segment->primary_id(undef); # this updates the object and expands its start and end positions without writing
# the segments into the database as individual objects
$parent->add_segment($segment); } $parent->add_segment($child); 1; # for debugging
} # a conventional Bio::SeqFeature::Generic object - create a split location
else { my $current_location = $parent->location; if ($current_location->can('add_sub_Location')) { $current_location->add_sub_Location($child->location); } else { eval "require Bio::Location::Split" unless Bio::Location::Split->can('add_sub_Location'); my $new_location = Bio::Location::Split->new(); $new_location->add_sub_Location($current_location); $new_location->add_sub_Location($child->location); $parent->location($new_location); } }
}
parse_attributesdescriptionprevnextTop
sub parse_attributes {
  my $self = shift;
  my $att  = shift;

  unless ($att =~ /=/) {  # ouch! must be a GFF line
require Bio::DB::SeqFeature::Store::GFF2Loader unless Bio::DB::SeqFeature::Store::GFF2Loader->can('parse_attributes'); return $self->Bio::DB::SeqFeature::Store::GFF2Loader::parse_attributes($att); } my @pairs = map { my ($name,$value) = split '='; [$self->unescape($name) => $value]; } split ';',$att; my (%reserved,%unreserved); foreach (@pairs) { my $tag = $_->[0]; unless (defined $_->[1]) { warn "$tag does not have a value at GFF3 file line $.\n"; next; } my @values = split ',',$_->[1]; map {$_ = $self->unescape($_);} @values; if ($Special_attributes{$tag}) { # reserved attribute
push @{$reserved{$tag}},@values; } else { push @{$unreserved{$tag}},@values } } return (\%reserved,\%unreserved);
}
_remapdescriptionprevnextTop
sub _remap {
    my $self = shift;
    my ($ref,$start,$end,$strand) = @_;
    my $mapper = $self->coordinate_mapper;
    return ($ref,$start,$end,$strand) unless $mapper;

    my ($newref,$coords) = $mapper->($ref,[$start,$end]);
    return unless defined $coords->[0];
    if ($coords->[0] > $coords->[1]) {
	@{$coords} = reverse(@{$coords}); 
	$strand *= -1;
    }
    return ($newref,@{$coords},$strand);
}
_indexitdescriptionprevnextTop
sub _indexit {
 # override    my $self      = shift;
return $self->{load_data}{Helper}->indexit(@_);
}
_local2globaldescriptionprevnextTop
sub _local2global {
 # override    my $self      = shift;
return $self->{load_data}{Helper}->local2global(@_);
}
local_idsdescriptionprevnextTop
sub local_ids {
 # override    my $self = shift;
return $self->{load_data}{Helper}->local_ids(@_);
}
loaded_idsdescriptionprevnextTop
sub loaded_ids {
 # override    my $self = shift;
return $self->{load_data}{Helper}->loaded_ids(@_); } 1; __END__
}
General documentation
loadTop
 Title   : load
Usage : $count = $loader->load(@ARGV)
Function: load the indicated files or filehandles
Returns : number of feature lines loaded
Args : list of files or filehandles
Status : public
Once the loader is created, invoke its load() method with a list of
GFF3 or FASTA file paths or previously-opened filehandles in order to
load them into the database. Compressed files ending with .gz, .Z and
.bz2 are automatically recognized and uncompressed on the fly. Paths
beginning with http: or ftp: are treated as URLs and opened using the
LWP GET program (which must be on your path).
FASTA files are recognized by their initial ">" character. Do not feed
the loader a file that is neither GFF3 nor FASTA; I don't know what
will happen, but it will probably not be what you expect.
accessorsTop
The following read-only accessors return values passed or created during new():
 store()          the long-term Bio::DB::SeqFeature::Store object
tmp_store() the temporary Bio::DB::SeqFeature::Store object used during loading sfclass() the Bio::SeqFeatureI class fast() whether fast loading is active seq_chunk_size() the sequence chunk size verbose() verbose progress messages
Internal MethodsTop
The following methods are used internally and may be overidden by
subclasses.
    default_seqfeature_class
    
$class = $loader->default_seqfeature_class

    Return the default SeqFeatureI class (Bio::DB::SeqFeature).
BUGSTop
This is an early version, so there are certainly some bugs. Please
use the BioPerl bug tracking system to report bugs.
SEE ALSOTop
Bio::DB::SeqFeature::Store,
Bio::DB::SeqFeature::Segment,
Bio::DB::SeqFeature::NormalizedFeature,
Bio::DB::SeqFeature::GFF2Loader,
Bio::DB::SeqFeature::Store::DBI::mysql,
Bio::DB::SeqFeature::Store::berkeleydb
AUTHORTop
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2006 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.