def test_find_motif_matches_unaligned(self):
mode = "unaligned"
motif = self.MOTIFS[0].split("-")[0] # motif = ACCACC --> rc_motif = GGTGGT
rc_REF_STR = motif_tools.rev_comp_motif(self.REF_STR)
strand = 0
matches_list = read_scanner.find_motif_matches(mode,motif,rc_REF_STR,strand)
match1 = matches_list[0]
self.assertEqual((18, 24), match1.span()[:2])
def test_scan_motifs_unaligned(self): mode = "unaligned" strand = 0 rc_REF_STR = motif_tools.rev_comp_motif(self.REF_STR) r_IPD_VALS = self.IPD_VALS[::-1] motifs = set(self.MOTIFS) bi_motifs = set() opts = data.set_opts() barcode, kmers = read_scanner.scan_motifs(mode, r_IPD_VALS, rc_REF_STR, strand, motifs, bi_motifs, opts) self.assertTrue(barcode["ACCACC-0"]==(1, round(2.4,1)) and \ barcode["TGATCA-2"]==(1, round(2.2,1)) and \ barcode["GACNNNNNACC-1"]==(1, round(2.3,1)))
def test_walk_over_read_bipartite_unaligned(self):
mode = "unaligned"
opts = data.set_opts()
rc_REF_STR = motif_tools.rev_comp_motif(self.REF_STR)
r_IPD_VALS = self.IPD_VALS[::-1]
motifs = set([self.MOTIFS[2]])
subread_ipds = {}
for motif in motifs:
subread_ipds[motif] = []
strand = 0
subread_ipds = read_scanner.walk_over_read_bipartite(mode, subread_ipds, rc_REF_STR, r_IPD_VALS, strand, opts)
self.assertTrue(round(subread_ipds["GACNNNNNACC-1"][0],1)==2.3 )
def test_walk_over_read_unaligned(self):
mode = "unaligned"
opts = data.set_opts()
rc_REF_STR = motif_tools.rev_comp_motif(self.REF_STR)
r_IPD_VALS = self.IPD_VALS[::-1]
motifs = set(self.MOTIFS[:2])
subread_ipds = {}
for motif in motifs:
subread_ipds[motif] = []
strand = 0
k = 6
subread_ipds = read_scanner.walk_over_read(mode, subread_ipds, rc_REF_STR, r_IPD_VALS, strand, k, opts)
self.assertTrue(round(subread_ipds["ACCACC-0"][0],1)==2.4 and \
round(subread_ipds["TGATCA-2"][0],1)==2.2)
def test_rev_comp_motif(self):
motif = "ACTTGTTACA"
rev_comped_motif = motif_tools.rev_comp_motif(motif)
self.assertEqual("TGTAACAAGT",rev_comped_motif)