In [1]:
import ga4gh_client.client as client
c = client.HttpClient("http://1kgenomes.ga4gh.org")
Read group sets are logical containers for read groups similar to BAM.
We can obtain read group sets via a search_read_group_sets request. Observe that this request takes as it's main parameter dataset_id, which was obtained using the example in 1kg_metadata_service using a search_datasets request.
In [2]:
counter = 0
for read_group_set in c.search_read_group_sets(dataset_id="WyIxa2dlbm9tZXMiXQ"):
counter += 1
if counter < 4:
print "Read Group Set: {}".format(read_group_set.name)
print "id: {}".format(read_group_set.id)
print "dataset_id: {}".format(read_group_set.dataset_id)
print "Aligned Read Count: {}".format(read_group_set.stats.aligned_read_count)
print "Unaligned Read Count: {}\n".format(read_group_set.stats.unaligned_read_count)
for read_group in read_group_set.read_groups:
print " Read group:"
print " id: {}".format(read_group.id)
print " Name: {}".format(read_group.name)
print " Description: {}".format(read_group.description)
print " Biosample Id: {}\n".format(read_group.bio_sample_id)
else:
break
In [3]:
read_group_set = c.get_read_group_set(read_group_set_id="WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTE5Njc4Il0")
print "Read Group Set: {}".format(read_group_set.name)
print "id: {}".format(read_group_set.id)
print "dataset_id: {}".format(read_group_set.dataset_id)
print "Aligned Read Count: {}".format(read_group_set.stats.aligned_read_count)
print "Unaligned Read Count: {}\n".format(read_group_set.stats.unaligned_read_count)
for read_group in read_group_set.read_groups:
print " Read Group: {}".format(read_group.name)
print " id: {}".format(read_group.bio_sample_id)
print " bio_sample_id: {}\n".format(read_group.bio_sample_id)
In [4]:
for read_group in read_group_set.read_groups:
print "Alignment from {}\n".format(read_group.name)
alignment = c.search_reads(read_group_ids=[read_group.id], start=0, end=1000000, reference_id="WyJOQ0JJMzciLCIxIl0").next()
print " id: {}".format(alignment.id)
print " fragment_name: {}".format(alignment.fragment_name)
print " aligned_sequence: {}\n".format(alignment.aligned_sequence)
https://ga4gh-schemas.readthedocs.io/en/latest/schemas/read_service.proto.html