This example illustrates how to access the GA4GH variant service.
The GA4GH variant service interchanges variant data similar to that found in VCF. It includes metadata related to variant entries and calls, which are the observed genetic variations pertaining to a given sample.
In [1]:
import ga4gh_client.client as client
c = client.HttpClient("http://1kgenomes.ga4gh.org")
In [2]:
for variant_set in c.search_variant_sets(dataset_id="WyIxa2dlbm9tZXMiXQ"):
print "Variant Set: {}".format(variant_set.name)
print " id: {}".format(variant_set.id)
print " dataset_id: {}".format(variant_set.dataset_id)
print " reference_set_id: {}\n".format(variant_set.reference_set_id)
In [3]:
variant_set = c.get_variant_set(variant_set_id="WyIxa2dlbm9tZXMiLCJ2cyIsInBoYXNlMy1yZWxlYXNlIl0")
print "name: {}".format(variant_set.name)
print "dataset_id: {}".format(variant_set.dataset_id)
print "reference_set_id: {}".format(variant_set.reference_set_id)
for metadata in variant_set.metadata[0:3]:
print metadata
The metadata fields of a Variant Set message can be used to interpret fields annotated about a variant, which will be addressed later in this document.
In [4]:
counter = 0
for variant in c.search_variants(variant_set_id="WyIxa2dlbm9tZXMiLCJ2cyIsInBoYXNlMy1yZWxlYXNlIl0", reference_name="1", start=10176, end= 40176):
if counter > 5:
break
counter += 1
print "Variant id: {}...".format(variant.id[0:10])
print "Variant Set Id: {}".format(variant.variant_set_id)
print "Names: {}".format(variant.names)
print "Reference Chromosome: {}".format(variant.reference_name)
print "Start: {}, End: {}".format(variant.start, variant.end)
print "Reference Bases: {}".format(variant.reference_bases)
print "Alternate Bases: {}\n".format(variant.alternate_bases)
In [5]:
single_variant = c.get_variant(variant_id=variant.id)
print "idd: {}".format(single_variant.id)
print "Variant Set Id: {}".format(single_variant.variant_set_id)
print "Names: {}".format(single_variant.names)
print "Reference Name: {}".format(single_variant.reference_name)
print "Start: {}, End: {}".format(single_variant.start, single_variant.end)
print "Reference Bases: {}".format(single_variant.reference_bases)
print "Alternate Bases: {}\n".format(single_variant.alternate_bases)
for info in single_variant.info:
print "Key: {},\tValues: {}".format(info, single_variant.info[info].values[0].string_value)
Using the variant_set.metadata message we can interpret these annotations.
In [6]:
metadata_dictionary = {}
for metadata in variant_set.metadata:
metadata_dictionary[metadata.key] = metadata # Load the metadata elements into a dictionary
for key in single_variant.info:
metadata_entry = metadata_dictionary["INFO." + key]
print "\nKey: {} Value: {} Type: {}".format(
key,
single_variant.info[key].values[0].string_value,
metadata_entry.type)
print " " + metadata_entry.description
Call sets represent a sample's column in a VCF, or the collection of observed sequences from a particular variation analysis. The Thousand Genomes data presents the variation data of 2504 individuals through 2504 callsets. These Call Sets ca be used to construct queries for individual genomic variations.
In [7]:
counter = 0
list_of_callset_ids = [] # Will use this list near the end to make a search variants query
for call_set in c.search_call_sets(variant_set_id=single_variant.variant_set_id):
if counter > 3:
break
else:
counter += 1
list_of_callset_ids.append(call_set.id)
print "Call Set Name: {}".format(call_set.name)
print " id: {}".format(call_set.name)
print " bio_sample_id: {}".format(call_set.name)
print " variant_set_ids: {}\n".format(call_set.variant_set_ids)
In [8]:
call_set = c.get_call_set(call_set_id=call_set.id)
print call_set
In [9]:
for variant_with_calls in c.search_variants(call_set_ids=list_of_callset_ids, variant_set_id="WyIxa2dlbm9tZXMiLCJ2cyIsInBoYXNlMy1yZWxlYXNlIl0", reference_name="1", start=10176, end= 10502):
print "Variant Id: {}".format(variant_with_calls.id)
print "Variant Set Id: {}".format(variant_with_calls.variant_set_id)
print "Names:{}".format(variant_with_calls.names)
print "Reference Chromosome: {}".format(variant_with_calls.reference_name)
print "Start: {}, End: {}".format(variant_with_calls.start, variant_with_calls.end)
print "Reference Bases: {}".format(variant_with_calls.reference_bases)
print "Alternate Bases: {}\n".format(variant_with_calls.alternate_bases)
for call in variant_with_calls.calls:
print " Call Set Name: {}".format(call.call_set_name)
print " Genotype: {}".format(call.genotype)
print " Phase set: {}".format(call.phaseset)
print " Call Set Id: {}\n".format(call.call_set_id)
https://ga4gh-schemas.readthedocs.io/en/latest/schemas/variant_service.proto.html