def read_data(self):
try:
data = UrlReader(self.URL).read()
except Exception:
data = self._read_cached_data()
if data is None:
return
else:
dir_path = local_cache_path(self.DIR_NAME)
if not os.path.exists(dir_path):
os.makedirs(dir_path)
data.save(local_cache_path(self.FILE_NAME))
self.set_source(data)
self.commit()
for dataset in mart.datasets():
print("\t\t Dataset '%s' %s' '%s'" % \
(dataset.datasetType, dataset.internalName,
dataset.displayName))
except BioMartError as err:
print(err, file=sys.stderr)
reg = BioMartRegistry(con)
dataset = reg.dataset("scerevisiae_gene_ensembl")
query = BioMartQuery(
con,
dataset="scerevisiae_gene_ensembl",
attributes=["ensembl_transcript_id", "transcript_exon_intron"],
filters=[("chromosome_name", "I"), ("with_wikigene", {
"excluded": "1"
})],
format="FASTA")
print(query.xml_query())
print(query.run())
data = query.get_table()
data.save("seq.tab")
import doctest
doctest.testmod(extraglobs={
"connection": con,
"registry": registry
},
optionflags=doctest.ELLIPSIS)
for schema in registry.virtual_schemas():
print("Virtual schema '%s'" % schema.name)
for mart in schema.databases():
print("\tMart: '%s' ('%s'):" % (mart.name, mart.displayName))
try:
for dataset in mart.datasets():
print("\t\t Dataset '%s' %s' '%s'" % \
(dataset.datasetType, dataset.internalName,
dataset.displayName))
except BioMartError as err:
print(err, file=sys.stderr)
reg = BioMartRegistry(con)
dataset = reg.dataset("scerevisiae_gene_ensembl")
query = BioMartQuery(
con, dataset="scerevisiae_gene_ensembl",
attributes=["ensembl_transcript_id", "transcript_exon_intron"],
filters=[("chromosome_name", "I"),
("with_wikigene", {"excluded": "1"})],
format="FASTA")
print(query.xml_query())
print(query.run())
data = query.get_table()
data.save("seq.tab")
import doctest
doctest.testmod(extraglobs={"connection": con, "registry": registry},
optionflags=doctest.ELLIPSIS)