def read_transfac(cls, fin, alphabet=None):
"""Parse a TRANSFAC-format PWM from a file.
Returns a Motif object, representing the provided
PWM along with an inferred or provided alphabet.
"""
items = []
start = False
for line in fin:
if line.isspace() or line[0] == "#":
continue # pragma: no cover
stuff = line.split()
if stuff[0] == "PO" or stuff[0] == "P0":
start = True
# 'XX' delimiters may precede the first motif
if start:
if stuff[0] in cls._TRANSFAC_DELIM_LINES:
break
else:
items.append(stuff)
if len(items) < 2:
raise ValueError("Vacuous file.")
# Is the first line a header line?
header = items.pop(0)
hcols = len(header)
rows = len(items)
cols = len(items[0])
if not (header[0] == "PO" or header[0] == "P0" or hcols == cols - 1
or hcols == cols - 2):
raise ValueError("Missing header line!") # pragma: no cover
# Do all lines (except the first) contain the same number of items?
cols = len(items[0])
for i in range(1, len(items)):
if cols != len(items[i]):
raise ValueError("Inconsistant length, row: {}".format(
i)) # pragma: no cover
# Vertical or horizontal arrangement?
if header[0] == "PO" or header[0] == "P0":
header.pop(0)
position_header = True
for h in header:
if not ischar(h):
raise ValueError("Expected a single character per header "
'item, but got "{}" as one item'.format(
h)) # pragma: no cover
if not isint(h):
position_header = False
alphabet_header = False if position_header else True
# Check row headers
if alphabet_header:
for i, r in enumerate(items):
if not isint(r[0]) and r[0][0] != "P":
raise ValueError("Expected position "
"as first item on line {}".format(
i)) # pragma: no cover
r.pop(0)
defacto_alphabet = "".join(header)
else:
a = [] # pragma: no cover
for i, r in enumerate(items): # pragma: no cover
if not ischar(r[0]) and r[0][0] != "P": # pragma: no cover
raise ValueError("Expected position " # pragma: no cover
"as first item on line {}".format(
i)) # pragma: no cover
a.append(r.pop(0)) # pragma: no cover
defacto_alphabet = "".join(a) # pragma: no cover
# Check defacto_alphabet
defacto_alphabet = Alphabet(defacto_alphabet)
if alphabet:
alphabet = Alphabet(alphabet)
if not defacto_alphabet.alphabetic(alphabet):
# Allow alphabet to be a superset of defacto_alphabet
alphabet = defacto_alphabet
else:
alphabets = (
unambiguous_rna_alphabet,
unambiguous_dna_alphabet,
unambiguous_protein_alphabet,
)
for a in alphabets:
if defacto_alphabet.alphabetic(a):
alphabet = a
break
if not alphabet:
alphabet = defacto_alphabet # pragma: no cover
# The last item of each row may be extra cruft. Remove
if len(items[0]) == len(header) + 1:
for r in items:
r.pop()
# items should now be a list of lists of numbers (as strings)
rows = len(items)
cols = len(items[0])
matrix = np.zeros((rows, cols), dtype=np.float64)
for r in range(rows):
for c in range(cols):
matrix[r, c] = float(items[r][c])
if position_header:
matrix.transpose() # pragma: no cover
return Motif(defacto_alphabet, matrix).reindex(alphabet)
def test_alphabet_alphabetic(self):
a = Alphabet("alphbet")
self.assertTrue(a.alphabetic("alphbet"))
self.assertTrue(not a.alphabetic("alphbetX"))
