#!/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. Feature Types # Get the list of all feature types in the Mouse eFG. For each one print its name, class and description # Get the list of all Mouse feature types with class 'Transcription Factor'. How many transcription factors are there? #Grab the eFG adaptor my $fta = $registry->get_adaptor('Mouse', 'funcgen', 'featuretype'); my @mouse_feature_types = @{$fta->fetch_all()}; foreach my $feature_type (@mouse_feature_types){ print $feature_type->name."\t".$feature_type->class."\t".$feature_type->description."\n"; } my @tfs = @{$fta->fetch_all_by_class('Transcription Factor')}; print scalar(@tfs)." transcription factors in the mouse eFG\n"; __END__ >perl metadata_2.pl H4ac Histone Histone 4 Acetylation H3ac Histone Histone 3 Acetylation H3K9ac Histone Histone 3 Lysine 9 Acetylation H3K4me3 Histone Histone 3 Lysine 4 Tri-Methylation H3K4me2 Histone Histone 3 Lysine 4 Di-Methylation H3K4me1 Histone Histone 3 Lysine 4 Mono-Methylation H4K4me3 Histone Histone 4 Lysine 4 Tri-Methylation Gene Associated Regulatory Feature Gene like regulatory feature Promoter Associated Regulatory Feature Promoter like regulatory feature Non-Gene Associated Regulatory Feature Non-Gene like regulatory feature Unclassified Regulatory Feature Unclassified regulatory feature cisRED Search Region Search Region cisRED search region cisRED Regulatory Motif cisRED group motif set miRanda Target RNA miRanda microRNA target VISTA Target Search Region VISTA target region VISTA Enhancer Enhancer Enhancer identified by positive VISTA assay VISTA Target - Negative Search Region Enhancer negative region identified by VISTA assay cisRED Motif Regulatory Motif cisRED motif crtMmus200913 Regulatory Motif cisRED group crtMmus200731 Regulatory Motif cisRED group crtMmus200472 Regulatory Motif cisRED group crtMmus200738 Regulatory Motif cisRED group crtMmus200085 Regulatory Motif cisRED group crtMmus200761 Regulatory Motif cisRED group crtMmus200511 Regulatory Motif cisRED group crtMmus200727 Regulatory Motif cisRED group crtMmus200157 Regulatory Motif cisRED group crtMmus200777 Regulatory Motif cisRED group crtMmus200631 Regulatory Motif cisRED group crtMmus200042 Regulatory Motif cisRED group crtMmus201037 Regulatory Motif cisRED group crtMmus200736 Regulatory Motif cisRED group crtMmus200052 Regulatory Motif cisRED group crtMmus201023 Regulatory Motif cisRED group crtMmus200701 Regulatory Motif cisRED group crtMmus200394 Regulatory Motif cisRED group crtMmus200485 Regulatory Motif cisRED group crtMmus200792 Regulatory Motif cisRED group crtMmus200997 Regulatory Motif cisRED group crtMmus200450 Regulatory Motif cisRED group crtMmus200751 Regulatory Motif cisRED group crtMmus200773 Regulatory Motif cisRED group crtMmus200484 Regulatory Motif cisRED group crtMmus201009 Regulatory Motif cisRED group crtMmus200959 Regulatory Motif cisRED group crtMmus200449 Regulatory Motif cisRED group ... mmu-miR-872* RNA miRanda miRNA_target mmu-miR-485* RNA miRanda miRNA_target mmu-miR-294* RNA miRanda miRNA_target mmu-miR-203* RNA miRanda miRNA_target mmu-miR-196a* RNA miRanda miRNA_target mmu-miR-879* RNA miRanda miRNA_target mmu-miR-299* RNA miRanda miRNA_target PolIII Transcription Associated Regulatory Feature PolIII transcribed RNA gene associated regulatory feature cMyb Transcription Factor cMyb Transcription Factor Binding Max Transcription Factor Max Transcription Factor Binding NELFe Transcription Factor NELFe Transcription Factor Binding Rad21 Transcription Factor Rad21 Transcription Factor Binding USF2 Transcription Factor USF2 Transcription Factor Binding GFP DNA GFP Control Rbbp5 Transcription Factor Rbbp5 Transcription Factor Binding Wdr5 Transcription Factor Wdr5 Transcription Factor Binding negative DNA negative library 23 transcription factors in the mouse eFG DB