def test_find_window_repetition():
p = Pattern([1, 1])
sqs = SQS(Database([[1, 1, 1, 2, 1, 1, 1, 1]]))
list_window = [Window(p, 0, 1, 0), Window(p, 4, 5, 0), Window(p, 6, 7, 0)]
assert list_window == sqs.find_windows(p)
def test_find_window_simple():
p = Pattern([1, 2])
sqs = SQS(Database([[1, 2, 3, 1, 2, 3, 1, 2, 3]]))
list_window = [Window(p, 0, 1, 0), Window(p, 3, 4, 0), Window(p, 6, 7, 0)]
assert list_window == sqs.find_windows(p)
def test_add_1(ct):
t = Transaction([5, 2, 3])
p = Pattern(t)
ct.add(p)
assert p in ct.patternMap.keys()
assert ct.patternMap[p] == 0
assert p.usage == 1
assert p.support == 1 # maybe useless
def test_index_sequence():
p = Pattern([1, 2])
sqs = SQS(
Database([[1, 2, 3, 1, 2, 3],
[1, 2, 3, 4, 3, 2, 1, 2, 3, 4, 3, 2, 1, 1, 2],
[3, 4, 5, 3, 2, 1], [1, 2]]))
for w in sqs.find_windows(p):
print("Sequence:{0}|Index:{1}", w.sequence, w.first)
def sct():
sct = CodeTable()
sct.add(Pattern([1]))
sct.add(Pattern([2]))
sct.add(Pattern([3]))
sct.add(Pattern([4]))
sct.add(Pattern([5]))
sct.add(Pattern([8]))
sct.add(Pattern([9]))
return sct
def test_find_window_long():
p = Pattern([1, 2, 3, 4, 3, 2, 1])
sqs = SQS(
Database([[
1, 2, 3, 1, 2, 3, 1, 2, 3, 4, 3, 2, 1, 2, 3, 4, 3, 2, 1, 1, 2, 3,
4, 5, 3, 2, 1
]]))
list_window = []
list_window.append(Window(p, 6, 12, 0))
for w in sqs.find_windows(p):
print(w.first)
assert list_window == sqs.find_windows(p)
def make_standard_code_table(self):
"""
Make the standard code table of the database, i.e. Code table
composed of singleton item of database
:return: The Standard code table
:rtype: CodeTableSlim
"""
sct = CodeTable() # map pattern code
# On ajoute les singletons de la base à la SCT
for trans in self.data_collection:
for item in trans:
pattern = Pattern([item])
sct.add(pattern, trans)
return sct
from src.Pattern import Pattern
from src.data_writer import DataWriter
dataset = []
for i in range(30):
dataset.append(Pattern(acnum=i))
DataWriter.file_writer(DataWriter.antigen_data_format(dataset),
"data/antigen.tsv")
DataWriter.file_writer(DataWriter.pattern_data_format(dataset),
"data/pattern.tsv")
def union(self, pattern):
res = []
res.extend(self.elements)
res.extend(pattern.elements)
return Pattern(res)
def test_find_window_4():
p = Pattern([1, 1, 2])
sqs = SQS(Database([[1, 1, 1, 2]]))
for w in sqs.find_windows(p):
print(w.first)
import pytest
from src.CodeTable import CodeTable
from src.Transaction import Transaction
from src.Pattern import Pattern
import math
t1 = Transaction(
[1, 2,
3]) # Change the transactions creation process using item_collection
t2 = Transaction([5, 8, 9])
t3 = Transaction([2])
t4 = Transaction([1, 2, 3, 4])
p1 = Pattern(t1)
p2 = Pattern(t2)
p3 = Pattern(t3)
@pytest.fixture
def ct():
return CodeTable()
@pytest.fixture
def ct_full():
ct = CodeTable()
ct.add(p1)
ct.add(p2)
return ct