def test_bam2gff(self):
name_counter = Counter()
transcripts = []
bam_file = pkg_resources.resource_filename("Mikado.tests",
"test.reads.bam")
for record in AlignmentFile(bam_file, mode="rb"):
if record.is_unmapped is True:
continue
transcript = Transcript(record)
if name_counter.get(record.query_name):
name = "{}_{}".format(record.query_name,
name_counter.get(record.query_name))
else:
name = record.query_name
if name != transcript.id:
transcript.alias = transcript.id
transcript.id = name
transcript.parent = transcript.attributes[
"gene_id"] = "{0}.gene".format(name)
name_counter.update([record.query_name])
transcript.source = "bam2gtf"
transcripts.append(transcript)
self.assertEqual(len(transcripts), 4)
self.assertEqual(transcripts[0].strand, '-')
self.assertEqual(transcripts[1].strand, '+')
self.assertEqual(transcripts[2].strand, '+')
self.assertEqual(transcripts[3].strand, '-')
def test_get_external(self):
checked_conf = load_and_validate_config(None).copy()
checked_conf.pick.output_format.report_all_external_metrics = True
transcript = Transcript()
transcript.chrom = "15"
transcript.source = "protein_coding"
transcript.start = 47631264
transcript.end = 48051999
exons = [(47631264, 47631416), (47704590, 47704669),
(47762671, 47762742), (47893062, 47893093),
(47895572, 47895655), (48051942, 48051999)]
transcript.strand = "+"
transcript.add_exons(exons)
transcript.id = "ENST00000560636"
transcript.parent = "ENSG00000137872"
transcript2 = transcript.copy()
transcript2.id = "ENST00000560637"
checked_conf.scoring.scoring["attributes.tpm"] = MinMaxScore.Schema(
).load({
"rescaling": "max",
"default": 0,
"rtype": "float",
'multiplier': 4,
'use_raw': True,
'percentage': True
})
transcript.attributes["tpm"] = 10
int_source = ExternalSource('int', 'int', 0)
float_source = ExternalSource('float', 'float', 0)
bool_source = ExternalSource('bool', 'bool', 0)
raw_int_source = ExternalSource('raw_int', 'int', 1)
raw_float_source = ExternalSource('raw_float', 'float', 1)
raw_bool_source = ExternalSource('raw_bool', 'bool', 1)
int_score = External(1, 1, 10)
float_score = External(1, 2, 10.0)
bool_score = External(
1, 3, int(False)
) # We cast as int here following external.py serialize function
raw_int_score = External(1, 4, 8)
raw_float_score = External(1, 5, 8.0)
raw_bool_score = External(
1, 6, int(True)
) # We cast as int here following external.py serialize function
query = Query(transcript.id, transcript.cdna_length)
query2 = Query(transcript2.id, transcript2.cdna_length)
engine = create_engine("sqlite:///:memory:")
db.metadata.create_all(engine)
SessionMaker = sessionmaker(bind=engine)
session = SessionMaker()
session.add_all([
int_source, float_source, bool_source, raw_int_source,
raw_float_source, raw_bool_source
])
session.add_all([query, query2])
session.add_all([
int_score, float_score, bool_score, raw_int_score, raw_float_score,
raw_bool_score
])
session.commit()
sup = Superlocus(transcript, configuration=checked_conf)
sup.session = session
tid = transcript.id
self.assertIn(tid, sup.transcripts)
from collections import namedtuple
qobj = {1: namedtuple('t', field_names=('query_name'))}
qobj[1].query_name = 'ENST00000560636'
external = asyncio.run(sup.get_external(qobj, [1]))
self.assertEqual(
external, {
'ENST00000560636': {
'int': (10, False),
'float': (10.0, False),
'bool': (False, False),
'raw_int': (8, True),
'raw_float': (8.0, True),
'raw_bool': (True, True)
}
})
sup.configuration.pick.output_format.report_all_external_metrics = False
external = asyncio.run(sup.get_external(qobj, [1]))
self.assertEqual(len(external), 0)
# These are meaningless it's just to verify we are loading *only* these metrics.
# We should *NOT* have 'float' as it is not present in any section.
sup.configuration.scoring.scoring["external.int"] = MinMaxScore(
rescaling="max", filter=None)
sup.configuration.scoring.requirements.parameters[
"external.raw_float"] = SizeFilter(operator="gt", value=100)
sup.configuration.scoring.cds_requirements.parameters[
"external.raw_int"] = SizeFilter(operator="lt", value=1)
sup.configuration.scoring.as_requirements.parameters[
"external.raw_bool"] = SizeFilter(operator="lt", value=1)
sup.configuration.scoring.not_fragmentary.parameters[
"external.bool"] = SizeFilter(operator="ne", value=False)
external = asyncio.run(sup.get_external(qobj, [1]))
self.assertEqual(
external, {
'ENST00000560636': {
'int': (10, False),
'raw_float': (8.0, True),
'bool': (False, False),
'raw_int': (8, True),
'raw_bool': (True, True)
}
})
def test_retrieval(self):
engine = create_engine("sqlite:///:memory:")
db.metadata.create_all(engine)
SessionMaker = sessionmaker(bind=engine)
session = SessionMaker()
transcript = Transcript(accept_undefined_multi=True)
transcript.chrom = "15"
transcript.source = "protein_coding"
transcript.start = 47631264
transcript.end = 48051999
exons = [(47631264, 47631416), (47704590, 47704669),
(47762671, 47762742), (47893062, 47893093),
(47895572, 47895655), (48051942, 48051999)]
transcript.strand = "+"
transcript.add_exons(exons)
transcript.id = "ENST00000560636"
transcript.parent = "ENSG00000137872"
transcript2 = transcript.copy()
transcript2.id = "ENST00000560637"
chrom_one = Chrom("1", 10**8)
chrom_fifteen = Chrom("15", 5 * 10**8)
session.add_all([chrom_one, chrom_fifteen])
session.commit()
# junction_start, junction_end, name, strand, score, chrom_id)
# This junction is on a different chrom
junction_chrom_one = Junction(47704669 + 1, 47762671 - 1, "chrom_one",
"+", 10, chrom_one.chrom_id)
# This junction is too far away
outside_chrom_15 = Junction(47704669 - 10**6 + 1, 47762671 - 10**6 - 1,
"chrom_15_outside", "+", 10,
chrom_fifteen.chrom_id)
# This junction is in the right place but wrong strand
wrong_strand_chrom_15 = Junction(47704669 + 1, 47762671 - 1,
"chrom_15_wrong_strand", "-", 10,
chrom_fifteen.chrom_id)
# This one is correct
chrom_15_junction = Junction(47704669 + 1, 47762671 - 1, "chrom_15",
"+", 10, chrom_fifteen.chrom_id)
session.add_all([
junction_chrom_one, outside_chrom_15, wrong_strand_chrom_15,
chrom_15_junction
])
session.commit()
self.assertEqual(junction_chrom_one.chrom, "1")
for junc in [
outside_chrom_15, wrong_strand_chrom_15, chrom_15_junction
]:
self.assertEqual(junc.chrom, "15")
for strand, stranded in itertools.product(("+", "-", None),
(True, False)):
transcript.unfinalize()
transcript.strand = strand
transcript.finalize()
sup = Superlocus(transcript, stranded=stranded)
self.assertTrue(
(chrom_15_junction.junction_start, chrom_15_junction.end)
in sup.introns, (chrom_15_junction, sup.introns))
sup.session = session
asyncio.run(sup._load_introns())
if stranded is True and strand is not None:
self.assertEqual(
sup.locus_verified_introns,
{(chrom_15_junction.junction_start,
chrom_15_junction.junction_end, strand)},
(stranded, strand))
elif stranded is False:
self.assertEqual(
sup.locus_verified_introns,
{(chrom_15_junction.junction_start,
chrom_15_junction.junction_end,
chrom_15_junction.strand),
(wrong_strand_chrom_15.junction_start,
wrong_strand_chrom_15.junction_end,
wrong_strand_chrom_15.strand)}, (stranded, strand))
elif stranded is True and strand is None:
self.assertEqual(sup.locus_verified_introns, set())