def test5_motif_to_img(self):
""" Motif to img """
seqlogo = which("seqlogo")
if seqlogo:
m = Motif(self.pfm)
m.to_img("test/test.png", fmt="png", seqlogo=seqlogo)
self.assertTrue(os.path.exists("test/test.png"))
os.unlink("test/test.png")
else:
print("seqlogo not found, skipping.")
class OneMotif:
bases = ["A", "C", "G", "T"]
def __init__(self, motifid=None, name=None, counts=None):
self.id = motifid if motifid != None else "" #should be unique
self.name = name if name != None else "" #does not have to be unique
self.prefix = "" #output prefix set in set_prefix
self.counts = counts if counts != None else [
[] for _ in range(4)
] #counts, list of 4 lists (A,C,G,T) (each as long as motif)
self.strand = "+" #default strand is +
self.length = 0 #length of motif
#Set later
self.pfm = None
self.bg = np.array([0.25, 0.25, 0.25,
0.25]) #background set to equal by default
self.pssm = None #pssm calculated from get_pssm
self.threshold = None #threshold calculated from get_threshold
self.gimme_obj = None #gimmemotif obj
def __str__(self):
""" Used for printing """
return ("{0}".format(self.__dict__))
def set_prefix(self, naming="name_id"):
""" Set name to be used in 4th column and as output prefix """
if naming == "name":
prefix = self.name
elif naming == "id":
prefix = self.id
elif naming == "name_id":
prefix = self.name + "_" + self.id
elif naming == "id_name":
prefix = self.id + "_" + self.name
else:
prefix = "None"
self.prefix = filafy(prefix)
return (self)
def get_pfm(self):
self.pfm = self.counts / np.sum(self.counts, axis=0)
def get_gimmemotif(self):
""" Get gimmemotif object for motif
Reads counts from self.counts """
self.length = len(self.counts[0])
motif_rows = []
for pos_id in range(self.length):
row = [self.counts[letter][pos_id] for letter in range(4)
] # each row represents one position in motif ( A C G T )
motif_rows.append(row)
self.gimme_obj = Motif(
motif_rows) # generate gimmemotif motif instance
self.gimme_obj.id = self.id + " " + self.name
return (self)
def get_biomotif(self):
""" Get biomotif object for motif """
self.biomotif_obj = ""
def get_reverse(self):
""" Reverse complement motif """
if self.pfm is None:
self.get_pfm()
#Create reverse motif obj
reverse_motif = OneMotif() #empty
for att in ["id", "name", "prefix", "strand", "length"]:
setattr(reverse_motif, att, getattr(self, att))
reverse_motif.strand = "-" if self.strand == "+" else "+"
reverse_motif.pfm = MOODS.tools.reverse_complement(self.pfm, 4)
return (reverse_motif) #OneMotif object
def get_pssm(self, ps=0.01):
""" Calculate pssm from pfm """
if self.pfm is None:
self.get_pfm()
bg_col = self.bg.reshape((-1, 1))
pseudo_vector = ps * bg_col
pssm = np.log(
np.true_divide(self.pfm + pseudo_vector,
np.sum(self.pfm + pseudo_vector,
axis=0))) - np.log(bg_col)
pssm = tuple([tuple(row) for row in pssm])
self.pssm = pssm
def get_threshold(self, pvalue):
""" Get threshold for moods scanning """
if self.pssm is None:
self.get_pssmm()
self.threshold = MOODS.tools.threshold_from_p(self.pssm, self.bg,
pvalue, 4)
return (self)
def calc_bit_score(self):
""" Bits for logo plots (?) """
if self.pfm is None:
self.get_pfm()
pfm_arr = np.copy(self.pfm)
pfm_arr[pfm_arr == 0] = np.nan
#Info content per pos
entro = pfm_arr * np.log2(pfm_arr)
entro[np.isnan(entro)] = 0
info_content = 2 - (-np.sum(entro, axis=0)
) #information content per position in motif
self.bits = self.pfm * info_content
def logo_to_file(self, filename):
""" Plots the motif to pdf/png/jpg file """
ext = os.path.splitext(filename)[-1]
#Currently only working with pdf
filename = filename.replace(ext, ".pdf") #hack
if ext == "jpg":
filename[-3:] = "png"
warnings.warn(
"The 'jpg' format is not supported for motif image. Type is set tp 'png'"
)
self.gimme_obj.to_img(filename)
def logo_to_ax(self):
ax = None
#René TODO
pass
return (ax)