def downloadBioMarkers():
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/Hs_exon_tissue-specific_protein_coding.zip'
print 'Downloading BioMarker associations'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/BioMarkers/','')
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/Mm_gene_tissue-specific_protein_coding.zip'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/BioMarkers/','')
def downloadMiRDatabases(species):
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/'+species+'_microRNA-Ensembl-GOElite_strict.txt'
selected = ['Hs','Mm','Rn'] ### these are simply zipped where the others are not
### These files should be updated on a regular basis
if species in selected:
url = string.replace(url,'.txt','.zip')
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/microRNATargets/','')
else:
### Where strict is too strict
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/'+species+'_microRNA-Ensembl-GOElite_lax.txt'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/microRNATargets/','')
fln = string.replace(fln,'.zip','.txt')
return fln
def downloadDiseaseOntologyOBO():
print 'Downloading Disease Ontology structure and associations'
""" Unfortunately, we have to download versions that are not as frequently updated, since RGDs server
reliability is poor """
#url = 'ftp://rgd.mcw.edu/pub/data_release/ontology_obo_files/disease/CTD.obo'
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/CTD.obo'
### Includes congenital and environmental diseases - http://ctdbase.org/detail.go?type=disease&acc=MESH%3aD002318
fln,status = update.downloadSuppressPrintOuts(url,'OBO/','')
def downloadDiseaseOntologyGeneAssociations(selected_species):
if selected_species == None: sc = []
else: sc = selected_species
""" Unfortunately, we have to download versions that are not as frequently updated, since RGDs server
reliability is poor """
if 'Hs' in sc or len(sc)==0:
#url = 'ftp://rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/homo_genes_do'
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/homo_genes_do'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/Disease/','')
if 'Mm' in sc or len(sc)==0:
#url = 'ftp://rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/mus_genes_do'
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/mus_genes_do'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/Disease/','')
if 'Rn' in sc or len(sc)==0:
#url = 'ftp://rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/rattus_genes_do'
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/rattus_genes_do'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/Disease/','')
def downloadDomainAssociations(selected_species):
paths=[]
if selected_species != None: ### Restrict to selected species only
current_species_dirs=selected_species
else:
current_species_dirs = unique.read_directory('/'+database_dir)
for species in current_species_dirs:
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/Domains/'+species+'_Ensembl-Domain.gz'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/Domains/','txt')
if 'Internet' not in status:
paths.append((species,fln))
return paths
def importUniProtAnnotations(species_db):
base_url = 'http://www.altanalyze.org/archiveDBs/'
uniprot_ensembl_db={}
for species in species_db:
url = base_url+species+'/custom_annotations.txt'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/UniProt/'+species+'/','')
for line in open(fln,'rU').xreadlines():
data = cleanUpLine(line)
ens_gene,compartment,function,symbols,full_name,uniprot_name,uniprot_ids,unigene = string.split(data,'\t')
symbols = string.split(string.replace(symbols,'; Synonyms=',', '),', ')
uniprot_ensembl_db[species,uniprot_name] = ens_gene
species_extension = string.split(uniprot_name,'_')[-1]
full_name = string.split(full_name,';')[0]
if 'Transcription factor' in full_name:
symbols.append(string.split(full_name,'Transcription factor ')[-1]) ### Add this additional synonym to symbols
### Extend this database out to account for weird names in PAZAR
for symbol in symbols:
new_name = string.upper(symbol)+'_'+species_extension
if new_name not in uniprot_ensembl_db:
uniprot_ensembl_db[species,symbol+'_'+species_extension] = ens_gene
uniprot_ensembl_db[species,string.upper(symbol)] = ens_gene
return uniprot_ensembl_db
def downloadPAZARAssocations():
base_url = 'http://www.pazar.info/tftargets/'
filenames = getPAZARFileNames()
print 'Downloading Transcription Factor to Target associations'
source = 'raw'
r = 4; k = -1
for resource in filenames:
filename = filenames[resource]
url = base_url+filename
start_time = time.time()
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/PAZAR/','')
end_time = time.time()
if (end_time-start_time)>3: ### Hence the internet connection is very slow (will take forever to get everything)
downloadPreCompiledPAZAR() ### Just get the compiled symbol data instead
print '...access to source PAZAR files too slow, getting pre-compiled from genmapp.org'
source = 'precompiled'
break
k+=1
if r==k:
k=0
print '*',
print ''
return source
def downloadGOSlimOBO():
url = 'http://www.geneontology.org/GO_slims/goslim_pir.obo'
#url = 'http://www.geneontology.org/GO_slims/goslim_generic.obo' ### Missing
fln,status = update.downloadSuppressPrintOuts(url,'OBO/','')
def downloadPathwayCommons():
print 'Downloading PathwayCommons associations'
url = 'http://www.pathwaycommons.org/pc-snapshot/current-release/gsea/by_species/h**o-sapiens-9606-gene-symbol.gmt.zip'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/PathwayCommons/','')
def downloadPhenotypeOntologyGeneAssociations():
url = 'ftp://ftp.informatics.jax.org/pub/reports/HMD_HumanPhenotype.rpt'
#url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/HMD_HumanPhenotype.rpt'
### Mouse and human gene symbols and gene IDs (use the gene symbols)
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/Pheno/','')
def downloadPhenotypeOntologyOBO():
print 'Downloading Phenotype Ontology structure and associations'
url = 'ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology'
fln,status = update.downloadSuppressPrintOuts(url,'OBO/','')
def downloadKEGGPathways(species):
print "Integrating KEGG associations for "+species
url = 'http://www.genmapp.org/go_elite/Databases/KEGG/'+species+'-KEGG_20110518.zip'
### This is a fixed date resource since KEGG licensed their material after this date
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/KEGG/','')
def downloadAmadeusPredictions():
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/symbol-Metazoan-Amadeus.txt'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/Amadeus/','')
def downloadPreCompiledPAZAR():
""" Downloads the already merged symbol to TF file from PAZAR files """
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/tf-target.txt'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/PAZAR/symbol/','')
