def get_genes_from_Ensembl_pairwise(args, sourcedata, targetdata):
genelist = []
inputtype = args.inputType
firstspecies = args.firstspecies
secondspecies = args.secondspecies
if (firstspecies == None):
print "Argument -s1 <firstspeciesname> is required"
elif (secondspecies == None):
print "Argument -s2 <secondspeciesname> is required"
else:
account = HostAccount('ensembldb.ensembl.org', 'anonymous', '')
firstgenome = Genome(firstspecies, ENSEMBL_VERSION, account)
secondgenome = Genome(secondspecies, ENSEMBL_VERSION, account)
if (inputtype == "id"):
firstgeneid = args.firstgeneid
if (firstgeneid == None):
print "Argument -gid1 <firstgeneid> is required"
secondgeneid = args.secondgeneid
if (secondgeneid == None):
print "Argument -gid2 <secondgeneid> is required"
if (firstgeneid != None and secondgeneid != None):
print "Retreving Genes", firstgeneid, secondgeneid
firstgene = firstgenome.getGeneByStableId(StableId=firstgeneid)
secondgene = secondgenome.getGeneByStableId(
StableId=secondgeneid)
if (inputtype == "name"):
gene = args.gene
if (gene == None):
print "Argument -g <genename> is required"
else:
print "Retreving Genes", name, "from species", firstspecies, secondspecies
firstgene = get_gene_from_Ensembl_by_name(gene, firstgenome)
secondgene = get_gene_from_Ensembl_by_name(gene, secondgenome)
sourcedata += get_cds_data(firstgene) + get_cds_data(secondgene)
targetdata += get_gene_data(firstgene) + get_gene_data(secondgene)
return sourcedata, targetdata
def ensembl_to_hgnc(gene_list):
account = HostAccount('blackrussian', 'bioinfo', 'A29bcd1234#', port=3306)
human = Genome('human', Release=73, account=account)
hgnc_list = []
for gene in gene_list:
hgnc_list.append(human.getGeneByStableId(StableId=gene).Symbol)
hgnc_list = set(hgnc_list)
return hgnc_list
def ensembl_to_hgnc(gene_list):
account = HostAccount('blackrussian', 'bioinfo', 'A29bcd1234#', port=3306)
human = Genome('human', Release=73, account=account)
hgnc_list = []
for gene in gene_list:
hgnc_list.append(human.getGeneByStableId(StableId=gene).Symbol)
hgnc_list = set(hgnc_list)
return hgnc_list
def get_genes_from_Ensembl_multiple(args, sourcedata, targetdata):
inputtype = args.inputType
if (inputtype == "id"):
geneidlistfile = args.geneIdListFile
if (geneidlistfile == None):
print "Argument -gidlf <geneidlistfilename> is required"
else:
for line in open(geneidlistfile, "r").readlines():
parse = line.split("\n")[0].split(" ")
if (len(parse) > 1):
species = parse[0]
geneid = parse[1]
print "Retreving Gene", geneid
account = HostAccount('ensembldb.ensembl.org', 'anonymous',
'')
genome = Genome(species, ENSEMBL_VERSION, account)
gene = genome.getGeneByStableId(StableId=geneid)
sourcedata += get_cds_data(gene)
targetdata += get_gene_data(gene)
if (inputtype == "name"):
gene = args.gene
if (gene == None):
print "Argument -g <genename> is required"
specieslistfile = args.specieslistfile
if (specieslistfile == None):
print "Argument -slf <specieslistfilename> is required"
if (gene != None and specieslistfile != None):
for line in open(specieslistfile, "r").readlines():
parse = line.split("\n")[0].split(" ")
if (len(parse) > 0):
species = parse[0]
print "Retreving Gene", gene, "from species", species
account = HostAccount('ensembldb.ensembl.org', 'anonymous',
'')
genome = Genome(species, ENSEMBL_VERSION, account)
gene = get_gene_from_Ensembl_by_name(gene, genome)
sourcedata += get_cds_data(gene)
targetdata += get_gene_data(gene)
return sourcedata, targetdata
def main():
import os
script_dir = os.path.dirname(os.path.abspath(__file__))
""" Neccesary to log into the ensembl database """
import os
from cogent.db.ensembl import HostAccount
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
""" gathers the transcript id and protein sequence from gene """
sp = "zebrafish"
gn = "ENSDARG00000027279"
from cogent.db.ensembl import Genome
specie = Genome(Species=sp, Release="81", account=None)
gene = specie.getGeneByStableId(StableId=gn)
for tr in gene.Transcripts:
print(tr.StableId)
for ex in tr.Exons:
print(ex.Symbol)
import os
import sqlalchemy as sql
from cogent.db.ensembl import HostAccount, Genome
#account = HostAccount(*os.environ['ENSEMBL_ACCOUNT'].split())
if 'ENSEMBL_ACCOUNT' in os.environ:
host, username, password = os.environ['ENSEMBL_ACCOUNT'].split()
account = HostAccount(host, username, password)
else:
account = None
human = Genome('human', Release=69, account=account)
# BRCA1
gene = human.getGeneByStableId(StableId="ENSG00000167131")
# get the db tables we need
external_db = human.CoreDb.getTable("external_db")
object_xref = human.CoreDb.getTable("object_xref")
xref = human.CoreDb.getTable("xref")
# get the external db ID for refseq mrna
refseq_mrna_id = sql.select([external_db.c.external_db_id],
external_db.c.db_name.like('RefSeq_mRNA')).execute().fetchone()
# query for a specific transcript ID
print "Querying for mRNA REFSEQ entries for one transcript"
query = sql.select([object_xref, xref],
sql.and_(xref.c.xref_id==object_xref.c.xref_id,
object_xref.c.ensembl_id == 1345831,
human = Genome(Species='human', Release=Release, account=account)
print human
'''
A Note on Coordinate Systems
The positions employed on Ensembls web-site, and in their MySQL database differ
from those used internally by cogent.db.ensembl.In all cases where you are querying
cogent.db.ensembl objects directly inputting nucleotide positions you can indicate
you are using Ensembl coordinates by setting ensembl_coord=True.
If you are explicitly passing in a cogent.db.ensembl region, that argument has no effect.
'''
## Selecting Gene
#Via StableID
brca1 = human.getGeneByStableId(StableId='ENSG00000012048')
print brca1.Description
#Or gene symbol
genes = human.getGenesMatching(Symbol='brca2')
for gene in genes:
if gene.Symbol.lower() == 'brca2':
break
brca2 = gene # so we keep track of this reference for later on
print "Symbol\t", brca2.Symbol
print "Descr.\t", brca2.Description
print "gene\t", brca2
print "loc.\t", brca2.Location
print "length\t" ,len(brca2)
Release=80 from cogent.db.ensembl import Species, Genome human = Genome(Species='human', Release=Release, account=None) gene = human.getGeneByStableId(StableId='ENSG00000205274') print gene.Symbol
