def test_orthology(self):
"""Tests - __init__."""
# register multispecies organism
so_db = Db.objects.create(name="SO")
so_cv = Cv.objects.create(name="sequence")
# creating test RO term
ro_db = Db.objects.create(name="RO")
ro_cv = Cv.objects.create(name="relationship")
fo_db = Db.objects.create(name="ORTHOMCL_SOURCE")
fo_cv = Cv.objects.create(name="feature_property")
# test_dbxref = Dbxref.objects.create(accession='123456', db=test_db)
so_dbxref = Dbxref.objects.create(accession="357", db=so_db)
so_dbxref2 = Dbxref.objects.create(accession="358", db=so_db)
ro_dbxref = Dbxref.objects.create(accession="658", db=ro_db)
# creating test SO term
Cvterm.objects.create(
name="contained in",
cv=ro_cv,
dbxref=ro_dbxref,
is_obsolete=0,
is_relationshiptype=1,
)
ortho_dbxref = Dbxref.objects.create(accession="ORTHOMCL_SOURCE",
db=fo_db)
term = Cvterm.objects.create(
name="orthologous group",
cv=fo_cv,
dbxref=ortho_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
poly_cvterm = Cvterm.objects.create(
name="polypeptide",
cv=so_cv,
dbxref=so_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
Cvterm.objects.create(
name="protein_match",
cv=so_cv,
dbxref=so_dbxref2,
is_obsolete=0,
is_relationshiptype=0,
)
db_null = Db.objects.create(name="null")
null_dbxref = Dbxref.objects.create(db=db_null, accession="null")
null_cv = Cv.objects.create(name="null")
Cvterm.objects.create(
cv=null_cv,
name="null",
definition="",
dbxref=null_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
# need to insert organisms first
organism1 = Organism.objects.create(species="coerulea",
genus="Aquilegia",
abbreviation="Aco")
organism2 = Organism.objects.create(species="distachyon",
genus="Brachypodium",
abbreviation="Brd")
organism3 = Organism.objects.create(species="clementina",
genus="Citrus",
abbreviation="Ccl")
organism4 = Organism.objects.create(species="carota",
genus="Dacus",
abbreviation="Dca")
organism5 = Organism.objects.create(species="grandis",
genus="Eucalyptus",
abbreviation="Egr")
organism6 = Organism.objects.create(species="vesca",
genus="Fragaria",
abbreviation="Fve")
organism7 = Organism.objects.create(species="max",
genus="Glycine",
abbreviation="Gma")
organism8 = Organism.objects.create(species="fedtschenkoi",
genus="Kalanchoe",
abbreviation="Kld")
self.assertTrue(Organism.objects.filter(abbreviation="Aco").exists())
self.assertTrue(Organism.objects.filter(abbreviation="Brd").exists())
self.assertTrue(Organism.objects.filter(abbreviation="Ccl").exists())
self.assertTrue(Organism.objects.filter(abbreviation="Dca").exists())
self.assertTrue(Organism.objects.filter(abbreviation="Egr").exists())
self.assertTrue(Organism.objects.filter(abbreviation="Fve").exists())
self.assertTrue(Organism.objects.filter(abbreviation="Gma").exists())
self.assertTrue(Organism.objects.filter(abbreviation="Kld").exists())
# also need to insert Features from fasta file first.
# inserting: Aqcoe0131s0001.1.v3.1
db = Db.objects.create(name="FASTA_SOURCE")
acc1 = "Aqcoe0131s0001.1.v3.1"
dbxref1 = Dbxref.objects.create(db=db, accession=acc1)
feature1 = Feature.objects.create(
dbxref=dbxref1,
organism=organism1,
uniquename="Aqcoe0131s0001.1.v3.1",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc1,
dbxref__db__name="FASTA_SOURCE",
).exists())
# inserting: Bradi0180s00100.1.v3.1; Bradi2g20400.1.v3.1
acc2 = "Bradi0180s00100.1.v3.1"
dbxref2 = Dbxref.objects.create(db=db, accession=acc2)
Feature.objects.create(
dbxref=dbxref2,
organism=organism2,
uniquename="Bradi0180s00100.1.v3.1",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc2,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc3 = "Bradi2g20400.1.v3.1"
dbxref3 = Dbxref.objects.create(db=db, accession=acc3)
Feature.objects.create(
dbxref=dbxref3,
organism=organism2,
uniquename="Bradi2g20400.1.v3.1",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc3,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
# inserting: Ciclev10013963m.v1.0; Ciclev10013962m.v1.0;
# Ciclev10013970m.v1.0
acc4 = "Ciclev10013963m.v1.0"
dbxref4 = Dbxref.objects.create(db=db, accession=acc4)
feature4 = Feature.objects.create(
dbxref=dbxref4,
organism=organism3,
uniquename="Ciclev10013963m.v1.0",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc4,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc5 = "Ciclev10013962m.v1.0"
dbxref5 = Dbxref.objects.create(db=db, accession=acc5)
Feature.objects.create(
dbxref=dbxref5,
organism=organism3,
uniquename="Ciclev10013962m.v1.0",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc5,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc6 = "Ciclev10013970m.v1.0"
dbxref6 = Dbxref.objects.create(db=db, accession=acc6)
Feature.objects.create(
dbxref=dbxref6,
organism=organism3,
uniquename="Ciclev10013970m.v1.0",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc6,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
# inserting: DCAR_032182.v1.0.388; DCAR_031986.v1.0.388;
# DCAR_032223.v1.0.388; DCAR_000323.v1.0.388
acc7 = "DCAR_032182.v1.0.388"
dbxref7 = Dbxref.objects.create(db=db, accession=acc7)
Feature.objects.create(
dbxref=dbxref7,
organism=organism4,
uniquename="DCAR_032182.v1.0.388",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc7,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc8 = "DCAR_031986.v1.0.388"
dbxref8 = Dbxref.objects.create(db=db, accession=acc8)
Feature.objects.create(
dbxref=dbxref8,
organism=organism4,
uniquename="DCAR_031986.v1.0.388",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc8,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc9 = "DCAR_032223.v1.0.388"
dbxref9 = Dbxref.objects.create(db=db, accession=acc9)
feature9 = Feature.objects.create(
dbxref=dbxref9,
organism=organism4,
uniquename="DCAR_032223.v1.0.388",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc9,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc10 = "DCAR_000323.v1.0.388"
dbxref10 = Dbxref.objects.create(db=db, accession=acc10)
feature10 = Feature.objects.create(
dbxref=dbxref10,
organism=organism4,
uniquename="DCAR_000323.v1.0.388",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc10,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
# inserting: Eucgr.L02820.1.v2.0
acc11 = "Eucgr.L02820.1.v2.0"
dbxref11 = Dbxref.objects.create(db=db, accession=acc11)
Feature.objects.create(
dbxref=dbxref11,
organism=organism5,
uniquename="Eucgr.L02820.1.v2.0",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc11,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
# inserting: mrna13067.1-v1.0-hybrid.v1.1
acc12 = "mrna13067.1-v1.0-hybrid.v1.1"
dbxref12 = Dbxref.objects.create(db=db, accession=acc12)
Feature.objects.create(
dbxref=dbxref12,
organism=organism6,
uniquename="mrna13067.1-v1.0-hybrid.v1.1",
type=poly_cvterm,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc12,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
# inserting: Glyma.10G030500.1.Wm82.a2.v1; Glyma.10G053100.1.Wm82.a2.v1
acc13 = "Glyma.10G030500.1.Wm82.a2.v1"
dbxref13 = Dbxref.objects.create(db=db, accession=acc13)
Feature.objects.create(
dbxref=dbxref13,
organism=organism7,
uniquename="Glyma.10G030500.1.Wm82.a2.v1",
type_id=poly_cvterm.cvterm_id,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc13,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc14 = "Glyma.10G053100.1.Wm82.a2.v1"
dbxref14 = Dbxref.objects.create(db=db, accession=acc14)
feature14 = Feature.objects.create(
dbxref=dbxref14,
organism=organism7,
uniquename="Glyma.10G053100.1.Wm82.a2.v1",
type_id=poly_cvterm.cvterm_id,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc14,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc15 = "Glyma.10G008400.1.Wm82.a2.v1"
dbxref15 = Dbxref.objects.create(db=db, accession=acc15)
Feature.objects.create(
dbxref=dbxref15,
organism=organism7,
uniquename="Glyma.10G008400.1.Wm82.a2.v1",
type_id=poly_cvterm.cvterm_id,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc15,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
# inserting: Kaladp0598s0001.1.v1.1
acc16 = "Kaladp0598s0001.1.v1.1"
dbxref16 = Dbxref.objects.create(db=db, accession=acc16)
feature16 = Feature.objects.create(
dbxref=dbxref16,
organism=organism8,
uniquename="Kaladp0598s0001.1.v1.1",
type_id=poly_cvterm.cvterm_id,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc16,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
acc17 = "Kaladp0598s0002.1.v1.1"
dbxref17 = Dbxref.objects.create(db=db, accession=acc17)
feature17 = Feature.objects.create(
dbxref=dbxref17,
organism=organism8,
uniquename="Kaladp0598s0002.1.v1.1",
type_id=poly_cvterm.cvterm_id,
is_analysis=False,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
self.assertTrue(
Feature.objects.filter(
type__cv__name="sequence",
type__name="polypeptide",
dbxref__accession=acc17,
dbxref__db__name__in=["GFF_SOURCE", "FASTA_SOURCE"],
).exists())
# ########################
# store feature groups:
filename = "groups.txt"
organism, created = Organism.objects.get_or_create(
abbreviation="multispecies",
genus="multispecies",
species="multispecies",
common_name="multispecies",
)
source = "null"
soterm = "polypeptide"
test_orthology_loader = FeatureLoader(source=source, filename=filename)
# ####################
# test store groups
group1_name = "machado0001"
members1 = [
"Aqcoe0131s0001.1.v3.1",
"Bradi0180s00100.1.v3.1",
"Bradi2g20400.1.v3.1",
"Ciclev10013963m.v1.0",
"DCAR_032223.v1.0.388",
"UnknownProtein.v1.1",
]
test_orthology_loader.store_feature_groups(group=members1,
soterm=soterm,
term=term,
value=group1_name)
group2_name = "machado0002"
members2 = [
"Eucgr.L02820.1.v2.0",
"mrna13067.1-v1.0-hybrid.v1.1",
"Ciclev10013970m.v1.0",
"DCAR_031986.v1.0.388",
]
test_orthology_loader.store_feature_groups(group=members2,
soterm=soterm,
term=term,
value=group2_name)
group3_name = "machado0003"
members3 = [
"Glyma.10G030500.1.Wm82.a2.v1",
"Glyma.10G053100.1.Wm82.a2.v1",
"DCAR_032182.v1.0.388",
]
test_orthology_loader.store_feature_groups(group=members3,
soterm=soterm,
term=term,
value=group3_name)
group4_name = "machado0004"
members4 = ["Glyma.10G008400.1.Wm82.a2.v1", "", "UnknownProtein.v1.2"]
test_orthology_loader.store_feature_groups(group=members4,
soterm=soterm,
term=term,
value=group4_name)
group5_name = "machado0005"
members5 = ["DCAR_000323.v1.0.388", "Kaladp0598s0002.1.v1.1"]
test_orthology_loader.store_feature_groups(group=members5,
soterm=soterm,
term=term,
value=group5_name)
group6_name = "machado0006"
members6 = ["Kaladp0598s0001.1.v1.1", "UnknownProtein.v1.3"]
test_orthology_loader.store_feature_groups(group=members6,
soterm=soterm,
term=term,
value=group6_name)
group7_name = "machado0007"
members7 = ["UnknownProtein.v1.4"]
test_orthology_loader.store_feature_groups(group=members7,
soterm=soterm,
term=term,
value=group7_name)
# ###check if relationships exist###
# in a group (machado0001 and machado0005)
self.assertTrue(
Featureprop.objects.filter(feature_id=feature1.feature_id,
type_id=term,
value=group1_name).exists())
self.assertTrue(
Featureprop.objects.filter(feature_id=feature9.feature_id,
type_id=term,
value=group1_name).exists())
self.assertTrue(
Featureprop.objects.filter(feature_id=feature4.feature_id,
type_id=term,
value=group1_name).exists())
# another example group5
self.assertTrue(
Featureprop.objects.filter(feature_id=feature10.feature_id,
type_id=term,
value=group5_name).exists())
self.assertTrue(
Featureprop.objects.filter(feature_id=feature17.feature_id,
type_id=term,
value=group5_name).exists())
# another example:
# ###check if a relationship does not exist###
# between features from different groups (machado0004 and machado0003)
self.assertFalse(
Featureprop.objects.filter(feature_id=feature16.feature_id,
type_id=term,
value=group6_name).exists())
self.assertFalse(
Featureprop.objects.filter(feature_id=feature4.feature_id,
type_id=term,
value=group2_name).exists())
self.assertFalse(
Featureprop.objects.filter(feature_id=feature14.feature_id,
type_id=term,
value=group1_name).exists())
def test_load_coexpression_clusters(self):
"""Run tests of load_coexpression_pairs."""
"""Load 'mcl.clusters.txt' output result file from LSTrAP.
The 'mcl.clusters.txt' is a tab separated, headless file and have the
format as follows (each line is a cluster):
ath_coexpr_mcl_1: AT3G18715.1.TAIR10 AT3G08790.1.TAIR10
AT5G42230.1.TAIR10
ath_coexpr_mcl_1: AT1G27040.1.TAIR10 AT1G71692.1.TAIR10
ath_coexpr_mcl_1: AT5G24750.1.TAIR10
...
and so on.
The features need to be loaded previously or won't be registered."""
# register multispecies organism
test_organism = Organism.objects.create(
abbreviation="multispecies",
genus="multispecies",
species="multispecies",
common_name="multispecies",
)
# creating test SO term
test_db = Db.objects.create(name="SO")
test_cv = Cv.objects.create(name="sequence")
# creating test RO term
test_db2 = Db.objects.create(name="RO")
test_cv2 = Cv.objects.create(name="relationship")
test_cv3 = Cv.objects.create(name="feature_property")
# test_dbxref = Dbxref.objects.create(accession='123456', db=test_db)
test_dbxref2 = Dbxref.objects.create(accession="028", db=test_db)
test_dbxref3 = Dbxref.objects.create(accession="135", db=test_db)
test_dbxref4 = Dbxref.objects.create(accession="246", db=test_db2)
test_dbxref5 = Dbxref.objects.create(accession="579", db=test_db2)
test_dbxref6 = Dbxref.objects.create(accession="357", db=test_db)
test_dbxref7 = Dbxref.objects.create(accession="468", db=test_db)
Cvterm.objects.create(
name="mRNA",
cv=test_cv,
dbxref=test_dbxref3,
is_obsolete=0,
is_relationshiptype=0,
)
# Cvterm.objects.create(
# name='polypeptide', cv=test_cv, dbxref=test_dbxref,
# is_obsolete=0, is_relationshiptype=0)
# register features.
Cvterm.objects.create(
name="contained in",
cv=test_cv2,
dbxref=test_dbxref2,
is_obsolete=0,
is_relationshiptype=1,
)
Cvterm.objects.create(
name="correlated with",
cv=test_cv2,
dbxref=test_dbxref4,
is_obsolete=0,
is_relationshiptype=1,
)
term = Cvterm.objects.create(
name="coexpression group",
cv=test_cv3,
dbxref=test_dbxref5,
is_obsolete=0,
is_relationshiptype=0,
)
test_term = Cvterm.objects.create(
name="polypeptide",
cv=test_cv,
dbxref=test_dbxref6,
is_obsolete=0,
is_relationshiptype=0,
)
Cvterm.objects.create(
name="protein_match",
cv=test_cv,
dbxref=test_dbxref7,
is_obsolete=0,
is_relationshiptype=0,
)
db = Db.objects.create(name="FASTA_SOURCE")
test_featurename1 = "AT3G18715.1.TAIR10"
dbxref1 = Dbxref.objects.create(db=db, accession=test_featurename1)
test_feature1 = Feature.objects.create(
dbxref=dbxref1,
organism=test_organism,
uniquename=test_featurename1,
is_analysis=False,
type_id=test_term.cvterm_id,
is_obsolete=False,
timeaccessioned=datetime.now(),
timelastmodified=datetime.now(),
)
test_featurename2 = "AT3G08790.1.TAIR10"
dbxref2 = Dbxref.objects.create(db=db, accession=test_featurename2)
test_feature2 = Feature.objects.create(
dbxref=dbxref2,
organism=test_organism,
uniquename=test_featurename2,
is_analysis=False,
type_id=test_term.cvterm_id,
is_obsolete=False,
timeaccessioned=datetime.now(),
timelastmodified=datetime.now(),
)
test_featurename3 = "AT5G42230.1.TAIR10"
dbxref3 = Dbxref.objects.create(db=db, accession=test_featurename3)
test_feature3 = Feature.objects.create(
dbxref=dbxref3,
organism=test_organism,
uniquename=test_featurename3,
is_analysis=False,
type_id=test_term.cvterm_id,
is_obsolete=False,
timeaccessioned=datetime.now(),
timelastmodified=datetime.now(),
)
test_featurename4 = "AT1G27040.1.TAIR10"
dbxref4 = Dbxref.objects.create(db=db, accession=test_featurename4)
test_feature4 = Feature.objects.create(
dbxref=dbxref4,
organism=test_organism,
uniquename=test_featurename4,
is_analysis=False,
type_id=test_term.cvterm_id,
is_obsolete=False,
timeaccessioned=datetime.now(),
timelastmodified=datetime.now(),
)
test_featurename5 = "AT1G71692.1.TAIR10"
dbxref5 = Dbxref.objects.create(db=db, accession=test_featurename5)
test_feature5 = Feature.objects.create(
dbxref=dbxref5,
organism=test_organism,
uniquename=test_featurename5,
is_analysis=False,
type_id=test_term.cvterm_id,
is_obsolete=False,
timeaccessioned=datetime.now(),
timelastmodified=datetime.now(),
)
test_featurename6 = "AT5G24750.1.TAIR10"
dbxref6 = Dbxref.objects.create(db=db, accession=test_featurename6)
test_feature6 = Feature.objects.create(
dbxref=dbxref6,
organism=test_organism,
uniquename=test_featurename6,
is_analysis=False,
type_id=test_term.cvterm_id,
is_obsolete=False,
timeaccessioned=datetime.now(),
timelastmodified=datetime.now(),
)
# clusters setup
test_cluster1_name = "ath_coexpr_mcl_1"
test_cluster1 = [
test_featurename1, test_featurename2, test_featurename3
]
test_cluster2_name = "ath_coexpr_mcl_2"
test_cluster2 = [test_featurename4, test_featurename5]
test_cluster3_name = "ath_coexpr_mcl_3"
test_cluster3 = [test_featurename6]
test_filename = "mcl.clusters.dummy.txt"
source = "null"
test_coexpression_loader = FeatureLoader(source=source,
filename=test_filename)
soterm = "polypeptide"
test_coexpression_loader.store_feature_groups(group=test_cluster1,
soterm=soterm,
term=term,
value=test_cluster1_name)
test_coexpression_loader.store_feature_groups(group=test_cluster2,
soterm=soterm,
term=term,
value=test_cluster2_name)
test_coexpression_loader.store_feature_groups(group=test_cluster3,
soterm=soterm,
term=term,
value=test_cluster3_name)
# check entire cluster1 relationships (not in reverse)
self.assertTrue(
Featureprop.objects.filter(feature_id=test_feature1.feature_id,
type=term,
value=test_cluster1_name).exists())
self.assertTrue(
Featureprop.objects.filter(feature_id=test_feature3.feature_id,
type=term,
value=test_cluster1_name).exists())
self.assertTrue(
Featureprop.objects.filter(feature_id=test_feature2.feature_id,
type=term,
value=test_cluster1_name).exists())
# check cluster2 relationships
self.assertTrue(
Featureprop.objects.filter(feature_id=test_feature5.feature_id,
type=term,
value=test_cluster2_name).exists())
self.assertTrue(
Featureprop.objects.filter(feature_id=test_feature4.feature_id,
type=term,
value=test_cluster2_name).exists())
self.assertFalse(
Featureprop.objects.filter(feature_id=test_feature6.feature_id,
type=term,
value=test_cluster3_name).exists())