#!/usr/bin/env perl =head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut use strict; use warnings; use Bio::EnsEMBL::Registry; my $registry = 'Bio::EnsEMBL::Registry'; $registry->load_registry_from_db( -host => 'ensembldb.ensembl.org', -user => 'anonymous' ); #2. FeatureSets #Feature Sets hold processed data or features i.e. peak calls or the output of a high level analysis e.g. the Regulatory Build. #Print the name of the feature sets for the Human 'GM12878' cell type. #Print the name of the feature sets for the Human 'CTCF' feature type. #Is the Human FeatureSet 'VISTA enhancer set' associated to any cell type or feature type? #Is the VISTA FeatureSet associated to a DataSet? #Hint: Use fetch_by_product_FeatureSet. #Any idea why this is so? #Is the Human FeatureSet 'RegulatoryFeatures:MultiCell' associated to a DataSet? #Any idea why this is so? #Grab the eFG adaptor my $fsa = $registry->get_adaptor('Human', 'funcgen', 'featureset'); my $cta = $registry->get_adaptor('Human', 'funcgen', 'celltype'); #Print GM12878 cell type details my @GM12878_feature_sets = @{$fsa->fetch_all_by_CellType($cta->fetch_by_name('GM12878'))}; print "There are ".scalar(@GM12878_feature_sets)." feature sets for GM12878:\n"; foreach my $featureset (@GM12878_feature_sets){ print "\t".$featureset->name."\n"; } =pod There are 72 feature sets for GM12878: GM12878_CTCF_ENCODE_Broad_SWEmbl_R015_D150 GM12878_H3K9ac_ENCODE_Broad_SWEmbl_R015_D150 GM12878_H4K20me1_ENCODE_Broad_SWEmbl_R015_D150 GM12878_CTCF_ENCODE_Uta_SWEmbl_R015_D150 GM12878_H3K36me3_ENCODE_Broad_SWEmbl_R015_D150 GM12878_H3K4me3_ENCODE_Broad_SWEmbl_R015_D150 GM12878_H3K4me2_ENCODE_Broad_SWEmbl_R015_D150 GM12878_Gabp_ENCODE_Hudsonalpha_SWEmbl_R015_D150 GM12878_Srf_ENCODE_Hudsonalpha_SWEmbl_R015_D150 GM12878_Nrsf_ENCODE_Hudsonalpha_SWEmbl_R015_D150 GM12878_PolII_ENCODE_Hudsonalpha_SWEmbl_R015_D150 GM12878_H3K27me3_ENCODE_Broad_SWEmbl_R015_D150 GM12878_H3K27ac_ENCODE_Broad_SWEmbl_R015_D150 GM12878_H3K4me1_ENCODE_Broad_SWEmbl_R015_D150 GM12878_DNase1_ENCODE_Duke_SWEmbl_R0025_D150 GM12878_Cfos_ENCODE_Yale_SWEmbl_R015_D150 GM12878_Jund_ENCODE_Yale_SWEmbl_R015_D150 GM12878_PolII_ENCODE_Yale_SWEmbl_R015_D150 GM12878_PolIII_ENCODE_Yale_SWEmbl_R015_D150 GM12878_Max_ENCODE_Yale_SWEmbl_R015_D150 GM12878_DNase1_ENCODE_Uw_SWEmbl_R0025_D150 GM12878_H3K36me3_ENCODE_Uw_SWEMBL_R015 GM12878_BCL3_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_EBF_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_Egr1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_IRF4_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_p300_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_Pax5_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_Sin3Ak20_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_USF1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_ZBTB33_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_FAIRE_ENCODE_UNC_SWEMBL_R0025 GM12878_Yy1_ENCODE_Yale_SWEMBL_R015 GM12878_Cmyc_ENCODE_Uta_SWEMBL_R015 GM12878_PolII_ENCODE_Uta_SWEMBL_R015 GM12878_H3K27me3_ENCODE_Uw_SWEMBL_R015 GM12878_BATF_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_BCL11A_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_NFKB_ENCODE_Yale_SWEMBL_R015 GM12878_Rad21_ENCODE_Yale_SWEMBL_R015 GM12878_Tr4_ENCODE_Yale_SWEMBL_R015 GM12878_ZZZ3_ENCODE_Yale_SWEMBL_R015 GM12878_Pbx3_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_POU2F2_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_PU1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_SP1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_TAF1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_Tcf12_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_H3K36me3_ENCODE_Broad_ccat_histone GM12878_H3K36me3_ENCODE_Uw_ccat_histone GM12878_Cjun_ENCODE_Yale_SWEMBL_R015 GM12878_Cmyc_ENCODE_Yale_SWEMBL_R015 GM12878_H2AZ_ENCODE_Broad_SWEMBL_R015 GM12878_H3K79me2_ENCODE_Broad_SWEMBL_R015 GM12878_H3K9me3_ENCODE_Broad_SWEMBL_R015 GM12878_ATF3_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_BCLAF1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_ELF1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_ETS1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_MEF2A_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_MEF2C_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_Rad21_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_RXRA_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_SIX5_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_Yy1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_ZEB1_ENCODE_Hudsonalpha_SWEMBL_R015 GM12878_CTCF_ENCODE_Uw_SWEMBL_R015 GM12878_H3K4me3_ENCODE_Uw_SWEMBL_R015 GM12878_H3K27me3_ENCODE_Broad_CCAT_HISTONE GM12878_H3K27me3_ENCODE_Uw_CCAT_HISTONE Segmentation:GM12878 RegulatoryFeatures:GM12878 =cut #Print CTCF feature type details my $fta = $registry->get_adaptor('Human', 'funcgen', 'featuretype'); my @CTCF_feature_sets = @{$fsa->fetch_all_by_FeatureType($fta->fetch_by_name('CTCF'))}; print "\n\nThere are ".scalar(@CTCF_feature_sets)." feature sets for CTCF:\n"; foreach my $featureset (@CTCF_feature_sets){ print "\t".$featureset->name."\n"; } =pod There are 28 feature sets for CTCF: K562_CTCF_ENCODE_Broad_SWEmbl_R015_D150 CD4_CTCF_BarskiZhao_PMID17512414_SWEmbl_R015_D150 HepG2_CTCF_ENCODE_Uta_SWEmbl_R015_D150 GM12878_CTCF_ENCODE_Broad_SWEmbl_R015_D150 GM12878_CTCF_ENCODE_Uta_SWEmbl_R015_D150 NHEK_CTCF_ENCODE_Broad_SWEmbl_R015_D150 HeLa-S3_CTCF_ENCODE_Uta_SWEmbl_R015_D150 H1ESC_CTCF_ENCODE_Broad_SWEmbl_R015_D150 HUVEC_CTCF_ENCODE_Broad_SWEmbl_R015_D150 HepG2_CTCF_ENCODE_Uw_SWEmbl_R015_D150 GM06990_CTCF_ENCODE_Uw_SWEmbl_R015_D150 K562_CTCF_ENCODE_Uta_SWEmbl_R015_D150 HeLa-S3_CTCF_ENCODE_Uw_SWEMBL_R015 HUVEC_CTCF_ENCODE_Uw_SWEMBL_R015 K562_CTCF_ENCODE_Uw_SWEMBL_R015 NHEK_CTCF_ENCODE_Uw_SWEMBL_R015 HepG2_CTCF_ENCODE_Broad_SWEMBL_R015 HUVEC_CTCF_ENCODE_Uta_SWEMBL_R015 NHEK_CTCF_ENCODE_Uta_SWEMBL_R015 HMEC_CTCF_ENCODE_Uw_SWEMBL_R015 HMEC_CTCF_ENCODE_Broad_SWEMBL_R015 HSMM_CTCF_ENCODE_Broad_SWEMBL_R015 NH-A_CTCF_ENCODE_Broad_SWEMBL_R015 H1ESC_CTCF_ENCODE_Uta_SWEMBL_R015 H1ESC_CTCF_ENCODE_Hudsonalpha_SWEMBL_R015 HepG2_CTCF_ENCODE_Hudsonalpha_SWEMBL_R015 HeLa-S3_CTCF_ENCODE_Broad_SWEMBL_R015 GM12878_CTCF_ENCODE_Uw_SWEMBL_R015 =cut #Print VISTA sets details my $vista_set = $fsa->fetch_by_name('VISTA enhancer set'); print "\n\n".$vista_set->display_label."\n"; my $cell_type = ($vista_set->cell_type) ? $vista_set->cell_type->name : 'NON-DEFINED'; print "\tCell type:\t".$cell_type; my $ftype = ($vista_set->feature_type) ? $vista_set->feature_type->name : 'NON-DEFINED'; print "\tFeatureType:\t$ftype\n"; my $dsa = $registry->get_adaptor('Human', 'funcgen', 'dataset'); my $dset = $dsa->fetch_by_product_FeatureSet($vista_set); my $dataset = ($dset) ? $dset->name : 'NON-DEFINED'; print "\tDataSet:\t$dataset\n"; =pod VISTA Enhancers Cell type: NON-DEFINED FeatureType: VISTA Target DataSet: NON-DEFINED =cut __END__