diff --git a/BlastHit.py b/BlastHit.py
index 1926869c998655520ccd3d5b142ef477ac82efe4..3fbea0ebb9f34371ded56c063ec415132b463ecd 100644
--- a/BlastHit.py
+++ b/BlastHit.py
@@ -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]"
diff --git a/test_pyBlast.py b/test_pyBlast.py
index 721052f2ec0424cefe6045f7129ae5b6e0c39d9a..f6d0cb8cfbbf24fcda15190069e3db4ed0d4b151 100644
--- a/test_pyBlast.py
+++ b/test_pyBlast.py
@@ -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