# We can get the nameID of all the available projects in this OpenCGA demo installation
for project in oc.projects.search().get_results():
    print(project['id'])

# We can also get the nameID of all the available studies for in the project
for study in oc.studies.search(project='exomes_grch37').get_results():
    print(study['id'])

# Let'sWe assumecan ourget installationthe alreadyID hasfor beenall populatedthe andavailable wefamilies arein interestedthe in lookingstudy
for family # all the families containing a concrete disorder: 'Rod-cone dystrophy'. To fetch this data, we will need to:
family_query_response = oc.families.search(study="study1", limit=10, disorders="Rod-cone dystrophy", include="id,members.id")

# Running oc.families.search(disorders="Rod-cone dystrophy") with only the 'disorders' field would only work
# if only one project and one study has been defined. However, we expect that most of the OpenCGA installations
# will have more than one study, so we need to specify the families of which study we are looking for.

# Additionally, we are passing limit = 10 to limit the number of family results we want to fetch. Because this
# is an example, we are simply limiting the number of results to 10. 

# Finally, if we don't specify anything else, all the values from the Family will be fetched. When writing 
# scripts, we are normally interested in just a few fields of a whole entry, so adding the include/exclude fields
# will definitely help us getting the results faster as we will avoid sending data we are going to discard through
# the network. In this particular case, we are only interested in getting the Family id and the id of the members
# of the family. To know what fields you can include/exclude, please follow the data models we have defined.

# family_query_response is an instance of the QueryResponse class defined in the Python library. To read the fields,
# we could do the following:
family_query_response.time         # Get the time spent with the REST call
family_query_response.apiVersion   # Get the API version of the REST
family_query_response.queryOptions # Get the QueryOptions of the call (include/exclude, limit, skip, count...)
family_query_response.warning      # Get warning messages
family_query_response.error        # Get error messages
family_query_response.responses    # Get the responses (Array of QueryResults containing the data queried)

# We can iterate over all the results to print all the id's using the 'results()' method such as in the example below:
for family in family_query_response.results():
	print (family['id'])

# We could have this same behaviour if we run the following script, which is why 'results()' is that useful.
for query_result in family_query_response.responses:
	for family in query_result['results']:
		print (family['id'])

# If we want to know exactly the amount of results obtained, we can run:
family_query_response.num_results()

# Or let's say that instead of querying the data, we only wanted to get the number of families in the study with that disorder. In that case, we could:
family_count_response = oc.families.search(study="study1", disorders="Rod-cone dystrophy", count=True)

# And then get the number of matches by calling to the num_matches method:
family_count_response.num_matches()

# Now that we know how to work with the OpenCGA QueryResponse object, we will write a script to fetch all the variants 
# falling in the 'BMPR2'in oc.families.search(study='ceph_trio').get_results():
    print(family['id'])

# We can get the ID for all the available samples in the study
for sample in oc.samples.search(study='ceph_trio').get_results():
    print(sample['id'])

# We are interested in looking for all the families containing a particular disorder: "RETINITIS PIGMENTOSA-DEAFNESS SYNDROME"
family_query_response = oc.families.search(
    study='ceph_trio',  # name of the study where the families are stored
    limit=10,  # retrieve only the first 10 results
    disorders='RETINITIS PIGMENTOSA-DEAFNESS SYNDROME',  # name of the disorders of interest
    include='id'  # retrieve only these fields from the results
)

# If we want to know exactly the amount of families obtained, we can run:
print(family_query_response.get_num_results())

# Now we fetch all the variants falling in the "BMPR2" gene found in any member of the family.
# In this case, we will limit the variant query to a maximum
# of 10 results
excluding the# We also exclude sample information (sample informationincludeSamples=None) as it can be huge and would make this query much slower).
for family in oc.families.search(study="study1",limit=10,disorders="Rod-cone dystrophy",include="id").results() this query much slower
for family in family_query_response.get_results():
    print('Family: ' + family['id'])
    variant_response = oc.variant.query(study='ceph_trio', family=family['id'], gene='BMPR2', includeSamples=None, limit=10)
    if variant_response.get_num_results() > 0:
    print ("Family: " + family['id'])    for variant in variant_response.get_results():
           variant_response = oc.variant.query(family=family['id'], gene= 'BMPR2', study='study1', includeSamples=None, limit=10)
    if variant_response.num_total_results() > 0 print('{}:{}-{}\t{}'.format(variant['chromosome'], str(variant['start']), str(variant['end']), variant['type']))
    else:
        forprint('No variant results in variant_response.results():
            print (variant['chromosome'] + ":" + str(variant['start']) + "-" + str(variant['end']) + '\t' + variant['type'])
    else:
        print ("No variant results found")found')

# Now we are interested in getting the rs IDs for the first 10 variants for a particular sample
for variant in oc.variant.query(sample='NA12878', study='ceph_trio', limit=10).get_results():
    print(variant['id'])

# We can also get rs IDs for multiple samples
for variant in oc.variant.query(sample='NA12878,NA12891,NA12892', study='ceph_trio', limit=10).get_results():
    print(variant['id'])