def getProbeset2Location(database="hgu133plus2.db"):
'''build map with genomic coordinates for each probeset.
The mapping is not necessarily unique.
'''
R.library(database)
prefix = database[:-len(".db")]
contigs = dict(R(prefix + "CHRLENGTHS"))
# map is a Bimap object
result2start = R.toTable(R(prefix + "CHRLOC"))
result2end = R.toTable(R(prefix + "CHRLOCEND"))
mapping = collections.defaultdict(list)
# make sure order is the same
assert result2start["probe_id"] == result2end["probe_id"]
for probeset_id, contig, start, end in zip(result2start["probe_id"],
result2start["Chromosome"],
result2start["start_location"],
result2end["end_location"]):
if start < 0:
start = contigs[contig] - start
end = contigs[contig] - end
mapping[probeset_id].append((contig, start, end))
E.info("mappings: probes=%i, contigs=%i" % (
len(set(result2start["probe_id"])),
len(set(result2start["Chromosome"])),
))
return mapping
def getProbeset2Location(database="hgu133plus2.db"):
'''build map with genomic coordinates for each probeset.
The mapping is not necessarily unique.
'''
R.library(database)
prefix = database[:-len(".db")]
contigs = dict(R(prefix + "CHRLENGTHS"))
# map is a Bimap object
result2start = R.toTable(R(prefix + "CHRLOC"))
result2end = R.toTable(R(prefix + "CHRLOCEND"))
mapping = collections.defaultdict(list)
# make sure order is the same
assert result2start["probe_id"] == result2end["probe_id"]
for probeset_id, contig, start, end in zip(result2start["probe_id"],
result2start["Chromosome"],
result2start["start_location"],
result2end["end_location"]):
if start < 0:
start = contigs[contig] - start
end = contigs[contig] - end
mapping[probeset_id].append((contig, start, end))
E.info("mappings: probes=%i, contigs=%i" %
(len(set(result2start["probe_id"])),
len(set(result2start["Chromosome"])),
))
return mapping
def getProbeset2Gene(database):
'''build map relating a probeset to an ENSEMBL gene_id'''
prefix = database[:-len(".db")]
mapping = prefix + "ENSEMBL"
R.library(database)
# map is a Bimap object
m = R(mapping)
result = R.toTable(m)
mapping = collections.defaultdict(list)
for probeset_id, gene_id in zip(result["probe_id"], result["ensembl_id"]):
mapping[probeset_id].append(gene_id)
E.info("obtained %i mappings: probes=%i, genes=%i" %
(len(result), len(set(
result["probe_id"])), len(set(result["ensembl_id"]))))
return mapping
def getProbeset2Gene(database):
"""build map relating a probeset to an ENSEMBL gene_id"""
prefix = database[: -len(".db")]
mapping = prefix + "ENSEMBL"
R.library(database)
# map is a Bimap object
m = R(mapping)
result = R.toTable(m)
mapping = collections.defaultdict(list)
for probeset_id, gene_id in zip(result["probe_id"], result["ensembl_id"]):
mapping[probeset_id].append(gene_id)
E.info(
"obtained %i mappings: probes=%i, genes=%i"
% (len(result), len(set(result["probe_id"])), len(set(result["ensembl_id"])))
)
return mapping