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refactor biodb-to-json.pl to be a Bio::JBrowse::Cmd module, make the …
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…json it produces contain all available data fields. references #72
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@rbuels
rbuels committed May 29, 2012
1 parent a95e58b commit 7229432
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234 changes: 10 additions & 224 deletions bin/biodb-to-json.pl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,14 @@
#!/usr/bin/env perl
use strict;
use FindBin qw($RealBin);
use lib "$RealBin/../lib";
use JBlibs;

use Bio::JBrowse::Cmd::BioDBToJson;

exit Bio::JBrowse::Cmd::BioDBToJson->new(@ARGV)->run;

__END__
=head1 NAME
Expand Down Expand Up @@ -56,227 +66,3 @@ =head2 OPTIONS
=back
=cut

use strict;
use warnings;

use FindBin qw($RealBin);
use lib "$RealBin/../lib";
use JBlibs;

use Pod::Usage;

use Getopt::Long;
use Data::Dumper;
use GenomeDB;
use BioperlFlattener;
use ExternalSorter;

my ($confFile, $ref, $refid, $onlyLabel, $verbose, $nclChunk, $compress);
my $outdir = "data";
my $sortMem = 1024 * 1024 * 512;
my $help; my $quiet;
GetOptions("conf=s" => \$confFile,
"ref=s" => \$ref,
"refid=s" => \$refid,
"track=s" => \$onlyLabel,
"out=s" => \$outdir,
"v+" => \$verbose,
"nclChunk=i" => \$nclChunk,
"compress" => \$compress,
"sortMem=i" =>\$sortMem,
"help|?|h" => \$help,
"quiet|q" => \$quiet,
) or pod2usage();

pod2usage( -verbose => 2 ) if $help;
pod2usage( 'must provide a --conf argument' ) unless defined $confFile;

if (!defined($nclChunk)) {
# default chunk size is 50KiB
$nclChunk = 50000;
# $nclChunk is the uncompressed size, so we can make it bigger if
# we're compressing
$nclChunk *= 4 if $compress;
}

my $gdb = GenomeDB->new( $outdir );

# determine which reference sequences we'll be operating on
my @refSeqs = @{ $gdb->refSeqs };
if (defined $refid) {
@refSeqs = grep { $_->{id} eq $refid } @refSeqs;
die "Didn't find a refseq with ID $refid (have you run prepare-refseqs.pl to supply information about your reference sequences?)" if $#refSeqs < 0;
} elsif (defined $ref) {
@refSeqs = grep { $_->{name} eq $ref } @refSeqs;
die "Didn't find a refseq with name $ref (have you run prepare-refseqs.pl to supply information about your reference sequences?)" if $#refSeqs < 0;
}
die "run prepare-refseqs.pl first to supply information about your reference sequences" if $#refSeqs < 0;


# read our conf file
die "conf file '$confFile' not found or not readable" unless -r $confFile;
my $config = JsonGenerator::readJSON($confFile);

# open and configure the db defined in the config file
eval "require $config->{db_adaptor}; 1" or die $@;
my $db = eval {$config->{db_adaptor}->new(%{$config->{db_args}})} or warn $@;
die "Could not open database: $@" unless $db;
if (my $refclass = $config->{'reference class'}) {
eval {$db->default_class($refclass)};
}
$db->strict_bounds_checking(1) if $db->can('strict_bounds_checking');
$db->absolute(1) if $db->can('absolute');


foreach my $seg (@refSeqs) {
my $segName = $seg->{name};
print "\nworking on refseq $segName\n" unless $quiet;

# get the list of tracks we'll be operating on
my @tracks = defined $onlyLabel
? grep { $_->{"track"} eq $onlyLabel } @{$config->{tracks}}
: @{$config->{tracks}};

foreach my $trackCfg ( @tracks ) {
my $trackLabel = $trackCfg->{'track'};
print "working on track $trackLabel\n" unless $quiet;

my $mergedTrackCfg = assemble_track_config(
$config,
{ key => $trackLabel,
%$trackCfg,
compress => $compress,
},
);

print "mergedTrackCfg: " . Dumper( $mergedTrackCfg ) if $verbose && !$quiet;

my $track = $gdb->getTrack( $trackLabel, $mergedTrackCfg, $mergedTrackCfg->{key} )
|| $gdb->createFeatureTrack( $trackLabel,
$mergedTrackCfg,
$mergedTrackCfg->{key},
);

my @feature_types = @{$trackCfg->{"feature"}};
next unless @feature_types;

print "searching for features of type: " . join(", ", @feature_types) . "\n" if $verbose && !$quiet;
# get the stream of the right features from the Bio::DB
my $iterator = $db->get_seq_stream( -seq_id => $segName,
-type => \@feature_types);


# make the flattener, which converts bioperl features to arrayrefs
my $flattener = BioperlFlattener->new(
$trackCfg->{"track"},
$mergedTrackCfg,
[],
[],
);

# start loading the track
$track->startLoad(
$segName,
$nclChunk,
[ {
attributes => $flattener->featureHeaders,
isArrayAttr => { Subfeatures => 1 },
},
{
attributes => $flattener->subfeatureHeaders,
isArrayAttr => {},
},
],
);


# make a sorting object, incrementally sorts the
# features according to the passed callback
my $sorter = do {
my $startCol = BioperlFlattener->startIndex;
my $endCol = BioperlFlattener->endIndex;
ExternalSorter->new(
sub ($$) {
$_[0]->[$startCol] <=> $_[1]->[$startCol]
||
$_[1]->[$endCol] <=> $_[0]->[$endCol]
},
$sortMem
);
};

# go through the features and put them in the sorter
my $featureCount = 0;
while( my $feature = $iterator->next_seq ) {

# load the feature's name record into the track
if( my $namerec = $flattener->flatten_to_name( $feature, $segName ) ) {
$track->nameHandler->addName( $namerec );
}

# load the flattened feature itself into the sorted, so we
# can load the actual feature data in sorted order below
my $row = $flattener->flatten_to_feature( $feature );
$sorter->add( $row );
$featureCount++;
}
$sorter->finish();

print "got $featureCount features for $trackCfg->{track}\n" unless $quiet;
next unless $featureCount > 0;

# iterate through the sorted features in the sorter and
# write them out
while( my $row = $sorter->get ) {
$track->addSorted( $row );
}

# finally, write the entry in the track list for the track we
# just made
$gdb->writeTrackEntry( $track );
}
}

exit;

#############

sub assemble_track_config {
my ( $global_config, $track_config ) = @_;

# merge the config
my %cfg = (
%{$config->{"TRACK DEFAULTS"}},
%$track_config
);

# rename some of the config variables
my %renamed_keys = qw(
class className
subfeature_classes subfeatureClasses
urlTemplate linkTemplate
);
for ( keys %cfg ) {
if( my $new_keyname = $renamed_keys{ $_ } ) {
$cfg{ $new_keyname } = delete $cfg{ $_ };
}
}

# move some of the config variables to a nested 'style' hash
my %style_keys = map { $_ => 1 } qw(
subfeatureClasses
arrowheadClass
className
histCss
featureCss
linkTemplate
);
for ( keys %cfg ) {
if( $style_keys{$_} ) {
$cfg{style}{$_} = delete $cfg{$_};
}
}

return \%cfg;
}

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