Commit 0f29b09b authored by Tiago Grego's avatar Tiago Grego
Browse files

fixes to serializer sample scripts

parent 4548c1cc
......@@ -8,18 +8,18 @@
# Dumper chromosome 1 only for size/speed, takes about 20 minutes
#
$|++;
use strict;
use warnings;
use Data::Dumper;
use Getopt::Long;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::IO::Translator::EnsFeature;
use Bio::EnsEMBL::IO::Translator::Feature;
use Bio::EnsEMBL::IO::Writer::GFF3;
use Bio::EnsEMBL::IO::Object::GXFMetadata;
$|++;
my $dbhost = 'ensembldb.ensembl.org';
my $dbuser = 'anonymous';
my $dbpass;
......@@ -50,7 +50,7 @@ my $adaptor = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Slice" );
my $ga = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Gene" );
my $dba = $adaptor->db();
my $translator = Bio::EnsEMBL::IO::Translator::EnsFeature->new();
my $translator = Bio::EnsEMBL::IO::Translator::Feature->new();
my $serializer = Bio::EnsEMBL::IO::Writer::GFF3->new($translator);
$serializer->open($outfile);
......@@ -116,7 +116,7 @@ while(my $chromosome = shift @{$features}) {
$serializer->write($chromosome);
# Write out the end of section separator for the GFF3 (ie. ###)
$serializer->fwd_ref_delimeter();
# $serializer->fwd_ref_delimeter();
# Cycle through and print chromosomes, depends on DB ordering, not likely
# good for production
......@@ -143,7 +143,7 @@ while(my $chromosome = shift @{$features}) {
}
# Write out the end of section separator for the GFF3 (ie. ###)
$serializer->fwd_ref_delimeter();
# $serializer->fwd_ref_delimeter();
}
}
......@@ -8,19 +8,19 @@
# Dumper chromosome 1 only for size/speed, takes about 20 minutes
#
$|++;
use strict;
use warnings;
use Data::Dumper;
use Getopt::Long;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::IO::Translator::EnsFeature;
use Bio::EnsEMBL::IO::Translator::Feature;
use Bio::EnsEMBL::IO::Writer::GTF;
use Bio::EnsEMBL::IO::Object::GXFMetadata;
use Bio::EnsEMBL::IO::Object::GTF;
$|++;
my $dbhost = 'ensembldb.ensembl.org';
my $dbuser = 'anonymous';
my $dbpass;
......@@ -51,7 +51,7 @@ my $adaptor = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Slice" );
my $ga = Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "Gene" );
my $dba = $adaptor->db();
my $translator = Bio::EnsEMBL::IO::Translator::EnsFeature->new();
my $translator = Bio::EnsEMBL::IO::Translator::Feature->new();
my $serializer = Bio::EnsEMBL::IO::Writer::GTF->new($translator);
# Two ways to override the callback table
......
......@@ -3,8 +3,6 @@
# Sample VCF4 serializer using the new ensembl-io methodology.
#
$|++;
use strict;
use warnings;
#use Data::Dumper;
......@@ -14,6 +12,8 @@ use Bio::EnsEMBL::IO::Translator::SampleGenotypeFeature;
use Bio::EnsEMBL::IO::Writer::VCF4;
use Bio::EnsEMBL::IO::Object::VCF4Metadata;
$|++;
my $db_version = Bio::EnsEMBL::ApiVersion->software_version;
# Connect to the Ensembl Registry to access the databases
......
......@@ -3,8 +3,6 @@
# Sample VCF4 serializer using the new ensembl-io methodology.
#
$|++;
use strict;
use warnings;
#use Data::Dumper;
......@@ -14,6 +12,8 @@ use Bio::EnsEMBL::IO::Translator::StructuralVariationFeature;
use Bio::EnsEMBL::IO::Writer::VCF4;
use Bio::EnsEMBL::IO::Object::VCF4Metadata;
$|++;
my $db_version = Bio::EnsEMBL::ApiVersion->software_version;
# Connect to the Ensembl Registry to access the databases
......
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