def get_transcript(self, ensg):
"""Takes ENSG and RefSeq codes to find Ensembl transcript ID and peptide ID.
:param ensg: ENSG number.
:param refseq: RefSeq NM_ code.
:return: transcript and protein IDs.
"""
# 1) Connect to BioMart server.
server = BiomartServer("http://www.ensembl.org/biomart")
server.verbose = True # provides setting up details
new_list = []
# 2) Select dataset to check against. Not essential but quicker so BioMart doesn't need to search.
hs_genes = server.datasets['hsapiens_gene_ensembl']
# 3) This is like clicking Results on the BioMart website. Filter by ENSG and RefSeq to get transcript & peptide
results = hs_genes.search({
'filters': {'ensembl_gene_id': '%s' % ensg,
'refseq_mrna': '%s' % self.refseq},
'attributes': ['ensembl_transcript_id', 'ensembl_peptide_id']
}, header=1)
# 4) Convert to readable format and add relevant information to a list.
for line in results.iter_lines():
line = line.decode('utf-8')
new_list.append(line.split())
uni_transcript = new_list[1]
transcript = uni_transcript[0]
protein = uni_transcript[1]
return transcript, protein
def serverConnection(proxy=None, verbose=True):
server = BiomartServer("http://ensembl.gramene.org/biomart")
# if you are behind a proxy
if proxy is not None:
server.http_proxy = os.environ.get('http_proxy', proxy)
# set verbose to True to get some messages
server.verbose = verbose
return server
def server_connect(self):
connected = False
while not connected:
try:
server = BiomartServer("http://grch37.ensembl.org/biomart")
connected = True
except requests.exceptions.ConnectionError:
connected = False
print('Connection error')
server.verbose = True
self.hsapiens_snp = server.datasets['hsapiens_snp']
def GOquery(query, organism, gene_id):
# connect to server
server = BiomartServer("http://www.biomart.org/biomart")
# set verbose to True to get some messages
server.verbose = True
db = server.datasets[organism + '_gene_ensembl']
response = db.search({
'filters': {
gene_id: query
},
'attributes': [gene_id, 'with_go']
})
return response
def get_transcript(ensg, refseq):
server = BiomartServer("http://www.ensembl.org/biomart")
server.verbose = True
new_list = []
hs_genes = server.datasets['hsapiens_gene_ensembl']
results = hs_genes.search({
'filters': {'ensembl_gene_id': '%s' % ensg,
'refseq_mrna': '%s' % refseq},
'attributes': ['ensembl_transcript_id', 'ensembl_peptide_id']
}, header=1)
for line in results.iter_lines():
line = line.decode('utf-8')
new_list.append(line.split())
uni_transcript = new_list[1]
transcript = uni_transcript[0]
protein = uni_transcript[1]
return transcript, protein
def searchDataset(chrom, start, end):
from biomart import BiomartServer
server = BiomartServer("http://asia.ensembl.org/biomart")
server.verbose = True
ccrigri = server.datasets["ccrigri_gene_ensembl"]
response = ccrigri.search({
"filters": {
"chromosome_name": chrom,
"start": start,
"end": end
},
"attributes": [
"ensembl_gene_id", "ensembl_transcript_id", "refseq_mrna",
"external_gene_name", "start_position", "end_position",
"wikigene_description"
]
})
for i in response.iter_lines():
i = i.decode("utf-8")
return i
# RUN ==========================================================================
# GENE LIST
# ------------------------------------------------------------------------------
# Read gene list
gene_list = pd.read_csv(gene_list_file, header=None)[0].tolist()
# BioMaRt
# Connect to the server and prepare for querying
# ------------------------------------------------------------------------------
# Connect to biomart
server = BiomartServer("http://www.ensembl.org/biomart")
server.verbose = False
# Check available databases
#server.show_databases()
# Select Genes database
db = server.databases['ENSEMBL_MART_ENSEMBL']
# Check available datasets (species)
#db.show_datasets()
# Select H. sapiens dataset
ds = db.datasets['hsapiens_gene_ensembl']
# show all available filters and attributes of the 'uniprot' dataset
#ds.show_filters()
from biomart import BiomartServer
server = BiomartServer( "http://www.biomart.org/biomart" ) # if not behind a proxy, otherwise see: https://pypi.python.org/pypi/biomart/0.8.0
server.verbose = True # set verbose to True to get some messages
# run a search with custom filters and attributes (no header)
response = uniprot.search({
'filters': {
'accession': ['Q9FMA1', 'Q8LFJ9']
},
'attributes': [
'accession', 'protein_name'
]
})
#!/usr/bin/env python # https://pypi.python.org/pypi/biomart from biomart import BiomartServer #Connect to a Biomart Server server = BiomartServer( "http://www.biomart.org/biomart" ) # set verbose to True to get some messages server.verbose = True
