## Create a human genome browser

import D3GB, urllib.request

# Genome browser generation.
# It creates a genome browser ready to view in a Firefox browser.
# For a server version, ready to be shared with Apache as a Website, set server=True
gwas, headers = urllib.request.urlretrieve('http://d3gb.usal.es/docs/data/GWAS_Catalog')
gb = D3GB.genomebrowser('GRCh37.bands', mapTrack = gwas, directory = 'HumanGenomeBrowser')

# Genes track
genes, headers = urllib.request.urlretrieve('http://d3gb.usal.es/docs/data/refFlat')
gb.addTrack(genes, 'refFlat', 'exons', '#B8860B')

# PFAM track
pfam, headers = urllib.request.urlretrieve('http://d3gb.usal.es/docs/data/Pfam')
gb.addTrack(pfam, 'Pfam', 'domain', '#303030')

# GWAS track
gb.addTrack(gwas, 'GWAS_Catalog', 'value', '#A52A2A', [0,100])

# Adding vep annotated vcf
vcf, headers = urllib.request.urlretrieve('http://d3gb.usal.es/docs/data/trio_vep')
gb.addVCF(vcf,'trio_vep',('Existing_variation','Consequence','IMPACT','GMAF'))

# Adding tissue expression
for i in ('adipose_tissue', 'adrenal_gland', 'brain', 'heart', 'kidney', 'liver', 'lung', 'ovary', 'pancreas', 'sigmoid_colon', 'small_intestine', 'spleen', 'testis'):
  tissue, headers = urllib.request.urlretrieve('http://d3gb.usal.es/docs/data/'+i)
  gb.addTrack(tissue,i,'score')

# Genomic sequence loading
fasta, headers = urllib.request.urlretrieve('ftp://ftp.ensembl.org/pub/grch37/release-85/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz')
gb.addSequence(fasta)