def test_gappy_kernel_bigger_gap(self):
sequences = [Seq("ACGTCGATGC")]
gappy_kernel = gk(sequences,k=1,t=0,g=3, gapDifferent = False, sparse = False)
expected = np.array([[0,3,2,2,1,1,4,2,2,3,2,2,1,2,2,1]])
expected = expected.astype(float)
self.assertTrue(np.array_equal(expected, gappy_kernel))
def test_gappy_kernel_flanking(self):
sequences = [Seq("ACGTCGatgC")]
gappy_kernel = gk(sequences,k=1,t=0,g=1, gapDifferent = False, sparse = False, include_flanking = True)
expected = np.array([[0,1,2,1,1,0,2,1,1,2,0,2,0,2,2,0]])
expected = expected.astype(float)
self.assertTrue(np.array_equal(expected, gappy_kernel))
def test_gappy_kernel_reverse(self):
sequences = [Seq("ACGTCGATGC")]
gappy_kernel = gk(sequences,k=1,t=0,g=1, gapDifferent = False, reverse = True, sparse = False)
expected = np.array([[0,3,3,1,3,0,2,0,3,2,0,0,0,0,0,0]])
expected = expected.astype(float)
self.assertTrue(np.array_equal(expected, gappy_kernel))
def test_gappy_kernel(self):
sequences = [Seq("ACGTCGATGC"), Seq("GTCGATAGC"), Seq("GTCGaaagATAGC")]
gappy_kernel = gk(sequences,k=1,t=0,g=1, gapDifferent = False, sparse = False)
expected = np.array([[0,1,2,1,1,0,2,1,1,2,0,2,0,2,2,0],[1,1,1,1,1,0,1,0,1,2,0,2,1,1,2,0],[1,1,1,1,1,0,1,0,1,2,0,2,1,1,2,0]])
expected = expected.astype(float)
self.assertTrue(np.array_equal(expected, gappy_kernel))
def test_gappy_kernel_sparse(self):
sequences = [Seq("ACGTCGATGC"), Seq("GTCGATAGC"), Seq("GTCGaaagATAGC")]
gappy_kernel = gk(sequences,k=1,t=0,g=1, gapDifferent = False)
expected = np.array([[0,1,2,1,1,0,2,1,1,2,0,2,0,2,2,0],[1,1,1,1,1,0,1,0,1,2,0,2,1,1,2,0],[1,1,1,1,1,0,1,0,1,2,0,2,1,1,2,0]])
expected = expected.astype(float)
expected = csr_matrix(expected)
self.assertTrue(0 == (expected != gappy_kernel).getnnz())
def test_gappy_kernel_bigger_k(self):
sequences = [Seq("ACGTCG")]
gappy_kernel = gk(sequences,k=2,t=0,g=1, gapDifferent = False, sparse = False)
expected = np.zeros((1,256))
expected[0,27] = 1.0
expected[0,29] = 1.0
expected[0,109] = 1.0
expected[0,102] = 1.0
expected[0,182] = 1.0
self.assertTrue(np.array_equal(expected, gappy_kernel))
def MakeKmerGappy(file1,K,T,G):
ti= tempfile.NamedTemporaryFile(delete=False,mode='w+b')
dest=open(file1+"_gappy_kmers.csv","w")
sequences = list(SeqIO.parse(file1, "fasta"))
X1=gk(sequences,k=int(K),t=int(T),g=int(G))
scipy.io.mmwrite(ti,X1)
ti.seek(0)
cnt=0
KmerDict=OrderedDict()
FirstRow=[]
NameDict=OrderedDict()
NameDict=ExtractInfoFasta(file1)
for line in ti:
line=line.decode()
line=line.rstrip()
if cnt<3:
cnt+=1
else:
a=line.split()
if a[1] not in FirstRow:
FirstRow.append(a[1])
if a[0] not in KmerDict:
KmerDict[a[0]]={}
KmerDict[a[0]][a[1]]=str(float(a[2]))
dest.write("id,"+",".join(FirstRow)+",species")
dest.write("\n")
Ke=list(KmerDict.keys())
for i in Ke:
Li=[]
Li.append(NameDict[int(i)][0])
for j in FirstRow:
if KmerDict[i].get(j,"-9")=="-9":
Li.append("0")
else:
Li.append(str(int(float(KmerDict[i][j]))))
Li.append(NameDict[int(i)][1])
dest.write(",".join(Li))
dest.write("\n")
dest.close()
ti.close()