def test_get_reference_model_segmented_transcript_no_siblings_no_descendants_no_ancestors():
feature_model = {
"id": "NM_018195.3",
"type": "mRNA",
"location": {
"type": "range",
"start": {"type": "point", "position": 135},
"end": {"type": "point", "position": 3304},
"strand": 1,
},
}
assert feature_model == get_reference_model_segmented(
"NG_012337.1", "NM_018195.3", False, False, False
)
def test_get_reference_model_segmented_transcript_no_siblings_no_ancestors_descendants():
feature_model = {
"id": "NM_018195.3",
"type": "mRNA",
"location": {
"type": "range",
"start": {"type": "point", "position": 135},
"end": {"type": "point", "position": 3304},
"strand": 1,
},
"features": [
{
"id": "exon-NM_018195.3-1",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 135},
"end": {"type": "point", "position": 189},
"strand": 1,
},
},
{
"id": "exon-NM_018195.3-2",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 618},
"end": {"type": "point", "position": 3304},
"strand": 1,
},
},
{
"id": "NP_060665.3",
"type": "CDS",
"location": {
"type": "range",
"start": {"type": "point", "position": 135},
"end": {"type": "point", "position": 1126},
"strand": 1,
},
},
],
}
assert feature_model == get_reference_model_segmented(
"NG_012337.1", "NM_018195.3", False, False, True
)
def test_get_reference_model_segmented_transcript_no_siblings_ancestors_no_descendants():
feature_model = {
"id": "NG_012337.1",
"type": "record",
"location": {
"type": "range",
"start": {"type": "point", "position": 0},
"end": {"type": "point", "position": 15948},
},
"qualifiers": {
"mol_type": "genomic DNA",
"chromosome": "11",
"dbxref": "taxon:9606",
"map": "11q23",
"name": "11",
},
"features": [
{
"id": "C11orf57",
"type": "gene",
"location": {
"type": "range",
"start": {"type": "point", "position": 0},
"end": {"type": "point", "position": 3304},
"strand": 1,
},
"qualifiers": {"name": "C11orf57", "HGNC": "25569"},
"features": [
{
"id": "NM_018195.3",
"type": "mRNA",
"location": {
"type": "range",
"start": {"type": "point", "position": 135},
"end": {"type": "point", "position": 3304},
"strand": 1,
},
},
],
},
],
}
assert feature_model == get_reference_model_segmented(
"NG_012337.1", "NM_018195.3", False, True, False
)
def test_get_reference_model_segmented_record_no_siblings_ancestors_no_descendants():
feature_model = {
"id": "NG_012337.1",
"type": "record",
"location": {
"type": "range",
"start": {"type": "point", "position": 0},
"end": {"type": "point", "position": 15948},
},
"qualifiers": {
"mol_type": "genomic DNA",
"chromosome": "11",
"dbxref": "taxon:9606",
"map": "11q23",
"name": "11",
},
}
assert feature_model == get_reference_model_segmented(
"NG_012337.1", "NG_012337.1", False, True, False
)
def get(self):
"""Retrieve the reference model."""
return get_reference_model_segmented(**_args.parse_args())
def test_get_reference_model_segmented_gene_no_siblings():
feature_model = {
"id": "NG_012337.1",
"type": "record",
"location": {
"type": "range",
"start": {"type": "point", "position": 0},
"end": {"type": "point", "position": 15948},
},
"qualifiers": {
"mol_type": "genomic DNA",
"chromosome": "11",
"dbxref": "taxon:9606",
"map": "11q23",
"name": "11",
},
"features": [
{
"id": "SDHD",
"type": "gene",
"location": {
"type": "range",
"start": {"type": "point", "position": 5000},
"end": {"type": "point", "position": 13948},
"strand": 1,
},
"qualifiers": {
"name": "SDHD",
"synonym": ["CBT1", "PGL", "PGL1", "SDH4"],
"HGNC": "10683",
},
"features": [
{
"id": "id-SDHD-1",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 5000},
"end": {"type": "point", "position": 5113},
"strand": 1,
},
},
{
"id": "id-SDHD-2",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 6010},
"end": {"type": "point", "position": 6127},
"strand": 1,
},
},
{
"id": "id-SDHD-3",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 7020},
"end": {"type": "point", "position": 7165},
"strand": 1,
},
},
{
"id": "id-SDHD-4",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 12958},
"end": {"type": "point", "position": 13948},
"strand": 1,
},
},
{
"id": "NM_003002.2",
"type": "mRNA",
"location": {
"type": "range",
"start": {"type": "point", "position": 5000},
"end": {"type": "point", "position": 13948},
"strand": 1,
},
"features": [
{
"id": "exon-NM_003002.2-1",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 5000},
"end": {"type": "point", "position": 5113},
"strand": 1,
},
},
{
"id": "exon-NM_003002.2-2",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 6010},
"end": {"type": "point", "position": 6127},
"strand": 1,
},
},
{
"id": "exon-NM_003002.2-3",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 7020},
"end": {"type": "point", "position": 7165},
"strand": 1,
},
},
{
"id": "exon-NM_003002.2-4",
"type": "exon",
"location": {
"type": "range",
"start": {"type": "point", "position": 12958},
"end": {"type": "point", "position": 13948},
"strand": 1,
},
},
{
"id": "NP_002993.1",
"type": "CDS",
"location": {
"type": "range",
"start": {"type": "point", "position": 5061},
"end": {"type": "point", "position": 13124},
"strand": 1,
},
},
],
},
],
}
],
}
assert feature_model == get_reference_model_segmented("NG_012337.1", "SDHD", False)