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Commit 5ad46016 authored by Adrien Leger's avatar Adrien Leger
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Correct assertion test in BlastHit

parent c78adf4b
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BlastHit.py
View file @ 5ad46016
......@@ -35,32 +35,32 @@ class BlastHit(object):
q_id = "query",
s_id = "subject",
identity = 100,
length = 0,
length = 10,
mis = 0,
gap = 0,
q_start = 0,
q_end = 0,
s_start = 0,
s_end = 0,
q_start = 1,
q_end = 10,
s_start = 1,
s_end = 10,
evalue = 0,
bscore = 0,
q_seq = "ATCG"):
"""
Create a BlastHit object which is automatically added to the class tracking instance list
The object with the following parameters are required for object initialisation
@param q_id Query sequence name
@param s_id Subject sequence name
@param identity % of identity in the hit
@param length length of the hit
@param mis Number of mismatch in the hit
@param gap Number of gap in the hit
@param q_start Hit start position of the query
@param q_end Hit end position of the query
@param s_start Hit start position of the subject
@param s_end Hit end position of the subject
@param evalue E value of the alignement
@param bscore Bit score of the alignement
@param q_seq Sequence of the query aligned on the subject sequence
@param q_id Query sequence name [STR]
@param s_id Subject sequence name [STR]
@param identity % of identity in the hit [FLOAT 0:100]
@param length length of the hit [INT >=1]
@param mis Number of mismatch in the hit [INT >=0]
@param gap Number of gap in the hit [INT >=0]
@param q_start Hit start position of the query (1 based) [INT >=1]
@param q_end Hit end position of the query (1 based) [INT >=1]
@param s_start Hit start position of the subject (1 based) [INT >=1]
@param s_end Hit end position of the subject (1 based) [INT >=1]
@param evalue E value of the alignement [FLOAT >=0]
@param bscore Bit score of the alignement [FLOAT >=0]
@param q_seq Sequence of the query aligned on the subject sequence [STR]
"""
# Store parameters in self variables
......@@ -112,12 +112,12 @@ class BlastHit(object):
def _test_arg(self):
assert 0 <= self.identity <= 100, "Identity value out of range [0:100]"
assert self.length > -1, "length value out of range [>= 0]"
assert self.mis > -1, "mis value out of range [>= 0]"
assert self.gap > -1, "gap value out of range [>= 0]"
assert self.q_start > -1, "q_start value out of range [>= 0]"
assert self.q_end > -1, "q_end value out of range [>= 0]"
assert self.s_start > -1, "s_start value out of range [>= 0]"
assert self.s_end > -1, "s_end value out of range [>= 0]"
assert self.evalue > -1, "evalue value out of range [>= 0]"
assert self.bscore > -1, "bscore value out of range [>= 0]"
assert self.length >= 1, "length value out of range [>= 1]"
assert self.mis >= 0, "mis value out of range [>= 0]"
assert self.gap >= 0, "gap value out of range [>= 0]"
assert self.q_start >= 0, "q_start value out of range [>= 1]"
assert self.q_end >= 0, "q_end value out of range [>= 1]"
assert self.s_start >= 0, "s_start value out of range [>= 1]"
assert self.s_end >= 0, "s_end value out of range [>= 1]"
assert self.evalue >= 0, "evalue value out of range [>= 0]"
assert self.bscore >= 0, "bscore value out of range [>= 0]"
test_pyBlast.py
View file @ 5ad46016
......@@ -80,17 +80,17 @@ class rand_subject_query_files (object):
# Define parameters for the test_BlastHit function with a pytest decorator
@pytest.mark.parametrize("identity, length, mis, gap, q_start, q_end, s_start, s_end, evalue, bscore", [
(rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), rf(0,10), rf(0,100)),
pytest.mark.xfail((-1, ri(1,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), -1, ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), -1, ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), -1, ri(0,100), ri(0,100), ri(0,100), ri(0,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), -1, ri(0,100), ri(0,100), ri(0,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(0,100), -1, ri(0,100), ri(0,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), -1, ri(0,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), -1, rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), -1, rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), ri(0,100), rf(0,100), -1))
(rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(1,100), ri(1,100), ri(1,100), ri(1,100), rf(0,10), rf(0,100)),
pytest.mark.xfail((-1, ri(1,100), ri(0,100), ri(0,100), ri(1,100), ri(1,100), ri(1,100), ri(1,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), -1, ri(0,100), ri(0,100), ri(1,100), ri(1,100), ri(1,100), ri(1,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), -1, ri(0,100), ri(1,100), ri(1,100), ri(1,100), ri(1,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), -1, ri(1,100), ri(1,100), ri(1,100), ri(1,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), -1, ri(1,100), ri(1,100), ri(1,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(1,100), -1, ri(1,100), ri(1,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(1,100), ri(1,100), -1, ri(1,100), rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(1,100), ri(1,100), ri(1,100), -1, rf(0,100), rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(1,100), ri(1,100), ri(1,100), ri(1,100), -1, rf(0,100))),
pytest.mark.xfail((rf(0,100), ri(1,100), ri(0,100), ri(0,100), ri(1,100), ri(1,100), ri(1,100), ri(1,100), rf(0,100), -1))
])
# Test BlastHit success and with failure with various parameters
......
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