def test_filter_bacteriocins_2(self):
bacteriocins = [blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin1",
query="ACGTACGTTT",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12345",
sbjct="ACGTACGTTT",
sbjct_start = 100,
sbjct_end = 110,
strand = "-"),
blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin2",
query="ACGTACGTTT",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12345",
sbjct="ACGTACGTTT",
sbjct_start = 1000,
sbjct_end = 1010,
strand = "-"),
blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin3",
query="ACGTACGTTT",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12346",
sbjct="ACGTACGTTT",
sbjct_start = 100,
sbjct_end = 110,
strand = "-")]
genes = [blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "gene1",
query="AAAAAAAAAA",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12345",
sbjct="AAAAAAAAAA",
sbjct_start = 150,
sbjct_end = 160,
strand = "-"),
blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "gene2",
query="AAAAAAAAAA",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12346",
sbjct="AAAAAAAAAA",
sbjct_start = 1050,
sbjct_end = 1060,
strand = "-")]
radius = 10000
filtered,hoods = interval_filter.bacteriocins(bacteriocins,genes,radius)
#print '\n'.join(map(str,filtered))
#print '\n'.join(map(str,hoods))
self.assertEquals(3,len(filtered))
self.assertEquals(3,len(hoods))
self.assertTrue(bacteriocins[0] in filtered)
def test_filter_bacteriocins_1(self):
bacteriocins = [blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin1",
query="ACGTACGTTT",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12345",
sbjct="ACGTACGTTT",
sbjct_start = 100,
sbjct_end = 110,
strand = "-"),
blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin2",
query="ACGTACGTTT",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12345",
sbjct="ACGTACGTTT",
sbjct_start = 1000,
sbjct_end = 1010,
strand = "-"),
blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin3",
query="ACGTACGTTT",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12346",
sbjct="ACGTACGTTT",
sbjct_start = 100,
sbjct_end = 110,
strand = "-")]
genes = [blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "gene1",
query="AAAAAAAAAA",
query_start = 1,
query_end = 10,
sbjct_id = "NC_12345",
sbjct="AAAAAAAAAA",
sbjct_start = 150,
sbjct_end = 160,
strand = "-"),
blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "gene2",
query="AAAAAAAAAA",
query_start = 1,
query_end = 10,
sbjct_id = "org2",
sbjct="AAAAAAAAAA",
sbjct_start = 1050,
sbjct_end = 1060,
strand = "-")]
radius = 100
filtered,hoods = interval_filter.bacteriocins(bacteriocins,genes,radius)
self.assertEquals(1,len(filtered))
self.assertEquals(1,len(hoods))
self.assertTrue(bacteriocins[0] in filtered)
record = hoods[0]
start,end,refid,gene = record.sbjct_start,record.sbjct_end,record.query_id,record.strand
self.assertEquals(start,150)
self.assertEquals(end,160)
self.assertEquals(refid,"gene1")