In [1]:
from ga4gh.client import client
c = client.HttpClient("http://1kgenomes.ga4gh.org")
In [2]:
#Obtain dataSet id REF: -> `1kg_metadata_service`
dataset = c.search_datasets().next()
In [3]:
counter = 0
for rna_quant_set in c.search_rna_quantification_sets(dataset_id=dataset.id):
if counter > 5:
break
counter += 1
print(" id: {}".format(rna_quant_set.id))
print(" dataset_id: {}".format(rna_quant_set.dataset_id))
print(" name: {}\n".format(rna_quant_set.name))
In [4]:
single_rna_quant_set = c.get_rna_quantification_set(
rna_quantification_set_id=rna_quant_set.id)
print(" name: {}\n".format(single_rna_quant_set.name))
In [5]:
counter = 0
for rna_quant in c.search_rna_quantifications(
rna_quantification_set_id=rna_quant_set.id):
if counter > 5:
break
counter += 1
print("RNA Quantification: {}".format(rna_quant.name))
print(" id: {}".format(rna_quant.id))
print(" description: {}\n".format(rna_quant.description))
test_quant = rna_quant
Similar to RNA quantification sets, we can retrieve a single RNA quantification by specific id. This id was chosen arbitrarily from the returned results.
The RNA quantification reported contains details of the processing pipeline which include the source of the reads as well as the annotations used.
In [6]:
single_rna_quant = c.get_rna_quantification(
rna_quantification_id=test_quant.id)
print(" name: {}".format(single_rna_quant.name))
print(" read_ids: {}".format(single_rna_quant.read_group_ids))
print(" annotations: {}\n".format(single_rna_quant.feature_set_ids))
In [7]:
def getUnits(unitType):
units = ["", "FPKM", "TPM"]
return units[unitType]
counter = 0
for expression in c.search_expression_levels(
rna_quantification_id=test_quant.id):
if counter > 5:
break
counter += 1
print("Expression Level: {}".format(expression.name))
print(" id: {}".format(expression.id))
print(" feature: {}".format(expression.feature_id))
print(" expression: {} {}".format(expression.expression, getUnits(expression.units)))
print(" read_count: {}".format(expression.raw_read_count))
print(" confidence_interval: {} - {}\n".format(
expression.conf_interval_low, expression.conf_interval_high))
It is also possible to restrict the search to a specific feature or to request expression values exceeding a threshold amount.
In [8]:
counter = 0
for expression in c.search_expression_levels(
rna_quantification_id=test_quant.id, feature_ids=[]):
if counter > 5:
break
counter += 1
print("Expression Level: {}".format(expression.name))
print(" id: {}".format(expression.id))
print(" feature: {}\n".format(expression.feature_id))
Let's look for some high expressing features.
In [9]:
counter = 0
for expression in c.search_expression_levels(
rna_quantification_id=test_quant.id, threshold=1000):
if counter > 5:
break
counter += 1
print("Expression Level: {}".format(expression.name))
print(" id: {}".format(expression.id))
print(" expression: {} {}\n".format(expression.expression, getUnits(expression.units)))
In [ ]: