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core.contactmap match and match_naive functions now match_other=True … #114

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core.contactmap match and match_naive functions now match_other=True … #114

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55ad661
core.contactmap match and match_naive functions now match_other=True …
jjavier-bm Jun 1, 2022
9b45a33
minor fix conkit.core.contactmap.ContactMap.match
jjavier-bm Jun 1, 2022
46bd45e
minor fix conkit.core.contactmap.ContactMap.match 2
jjavier-bm Jun 1, 2022
953f818
remove trash backup file
jjavier-bm Jun 1, 2022
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22 changes: 12 additions & 10 deletions conkit/core/contactmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -738,13 +738,14 @@ def match_naive(self, other, add_false_negatives=False, match_other=False, inpla
else:
contact.false_positive = True

if not add_false_negatives:
if not add_false_negatives and not match_other:
return contact_map1

for contact in contact_map2:
if contact.id not in contact_map1_set:
contact.false_negative = True
contact_map1.add(contact)
if add_false_negatives:
contact_map1.add(contact)

return contact_map1

Expand Down Expand Up @@ -800,15 +801,16 @@ def match(self, other, add_false_negatives=False, match_other=False, remove_unma
else:
contact_map2 = other._inplace(False)

if contact_map1.empty and add_false_negatives:
if contact_map1.empty:
for contact in contact_map2:
contact.false_negative = True
if add_false_negatives:
contact_map1.add(contact)
return contact_map1

if contact_map2.empty:
for contact in contact_map1:
contact.false_positive = True

if contact_map2.empty or contact_map1.empty:
return contact_map1

# ================================================================
Expand Down Expand Up @@ -876,12 +878,12 @@ def match(self, other, add_false_negatives=False, match_other=False, remove_unma
# ================================================================
# 3. Add false negatives
# ================================================================
if add_false_negatives:
for contactid in contact_map2.as_list():
contactid = tuple(contactid)
if contactid not in contact_map1:
for contactid in contact_map2.as_list():
contactid = tuple(contactid)
if contactid not in contact_map1:
contact_map2[contactid].status = ContactMatchState.false_negative
if add_false_negatives:
contact = contact_map2[contactid].copy()
contact.false_negative = True
contact_map1.add(contact)

# ================================================================
Expand Down
60 changes: 60 additions & 0 deletions conkit/core/tests/test_contactmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -535,6 +535,7 @@ def test_match_4(self):

contact_map1.match(contact_map2, match_other=True, remove_unmatched=True, inplace=True)
self.assertEqual([TP, TP], [c.status for c in contact_map1])
self.assertEqual([TP, TP, FN], [c.status for c in contact_map2])
self.assertEqual([2, 2, 3], [c.res1_altseq for c in contact_map2])
self.assertEqual([6, 7, 5], [c.res2_altseq for c in contact_map2])

Expand Down Expand Up @@ -891,6 +892,27 @@ def test_match_14(self):
contact_map2.set_sequence_register()

contact_map1.match(contact_map2, add_false_negatives=True, inplace=True, match_other=True)
self.assertEqual([FN, FN, FN, FN], [c.status for c in contact_map1])
self.assertEqual([FN, FN, FN, FN], [c.status for c in contact_map2])
self.assertListEqual([[1, 5], [1, 7], [2, 7], [3, 4]], contact_map2.as_list())

def test_match_15(self):
contact_map1 = ContactMap("foo")
contact_map1.sequence = Sequence("foo", "AICDEFGH")
contact_map1.set_sequence_register()

contact_map2 = ContactMap("bar")
for i, params in enumerate([(1, 5, 1.0), (1, 7, 1.0), (2, 7, 1.0), (3, 4, 1.0)]):
contact = Contact(*params)
contact.res1_altseq = params[0]
contact.res2_altseq = params[1]
contact.status = TP
contact_map2.add(contact)
contact_map2.sequence = Sequence("bar", "AICDEFGH")
contact_map2.set_sequence_register()

contact_map1.match(contact_map2, inplace=True, match_other=True)
self.assertEqual([], [c.status for c in contact_map1])
self.assertEqual([FN, FN, FN, FN], [c.status for c in contact_map2])
self.assertListEqual([[1, 5], [1, 7], [2, 7], [3, 4]], contact_map2.as_list())

Expand Down Expand Up @@ -946,9 +968,47 @@ def test_match_naive_3(self):
contact_map2.set_sequence_register()

contact_map1.match_naive(contact_map2, add_false_negatives=True, inplace=True, match_other=True)
self.assertEqual([FN, FN, FN, FN], [c.status for c in contact_map1])
self.assertEqual([FN, FN, FN, FN], [c.status for c in contact_map2])
self.assertListEqual([[1, 5], [1, 7], [2, 7], [3, 4]], contact_map2.as_list())

def test_match_naive_4(self):
contact_map1 = ContactMap("foo")
for params in [(1, 5, 1.0), (1, 6, 1.0), (2, 7, 1.0), (3, 5, 1.0), (2, 8, 1.0)]:
contact = Contact(*params)
contact_map1.add(contact)

contact_map2 = ContactMap("bar")
for i, params in enumerate([(1, 5, 1.0), (1, 7, 1.0), (2, 7, 1.0), (3, 4, 1.0)]):
contact = Contact(*params)
contact.res1_altseq = params[0]
contact.res2_altseq = params[1]
contact.status = TP
contact_map2.add(contact)

contact_map1.match_naive(contact_map2, inplace=True, match_other=True)
self.assertEqual([TP, FP, TP, FP, FP], [c.status for c in contact_map1])
self.assertEqual([TP, FN, TP, FN], [c.status for c in contact_map2])

def test_match_naive_5(self):
contact_map1 = ContactMap("foo")
contact_map1.sequence = Sequence("foo", "AICDEFGH")
contact_map1.set_sequence_register()

contact_map2 = ContactMap("bar")
for i, params in enumerate([(1, 5, 1.0), (1, 7, 1.0), (2, 7, 1.0), (3, 4, 1.0)]):
contact = Contact(*params)
contact.res1_altseq = params[0]
contact.res2_altseq = params[1]
contact.status = TP
contact_map2.add(contact)
contact_map2.sequence = Sequence("bar", "AICDEFGH")
contact_map2.set_sequence_register()

contact_map1.match_naive(contact_map2, inplace=True, match_other=True)
self.assertEqual([], [c.status for c in contact_map1])
self.assertEqual([FN, FN, FN, FN], [c.status for c in contact_map2])

def test_remove_neighbors_1(self):
contact_map = ContactMap("test")
for c in [Contact(1, 5, 1.0), Contact(3, 3, 0.4), Contact(2, 4, 0.1), Contact(5, 1, 0.2)]:
Expand Down