def read_transfac( fin, alphabet = None) :
""" Parse a sequence matrix from a file.
Returns a tuple of (alphabet, matrix)
"""
items = []
start=True
for line in fin :
if line.isspace() or line[0] =='#' : continue
stuff = line.split()
if start and stuff[0] != 'PO' and stuff[0] != 'P0': continue
if stuff[0]=='XX' or stuff[0]=='//': break
start = False
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!"
# 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 %d: " % i
# Vertical or horizontal arrangement?
if header[0] == 'PO' or header[0] == 'P0': header.pop(0)
position_header = True
alphabet_header = True
for h in header :
if not isint(h) : position_header = False
if not str.isalpha(h) : alphabet_header = False
if not position_header and not alphabet_header :
raise ValueError, "Can't parse header: %s" % str(header)
if position_header and alphabet_header :
raise ValueError, "Can't parse header"
# Check row headers
if alphabet_header :
for i,r in enumerate(items) :
if not isint(r[0]) :
raise ValueError, "Expected position as first item on line %d", i
r.pop(0)
defacto_alphabet = ''.join(header)
else :
a = []
for i,r in enumerate(items) :
if not ischar(r[0]) :
raise ValueError, "Expected position as first item on line %d", i
a.append(r.pop(0))
defacto_alphabet = ''.join(a)
# Check defacto_alphabet
defacto_alphabet = Alphabet(defacto_alphabet)
if alphabet :
if not defacto_alphabet.alphabetic(alphabet) :
raise ValueError, "Incompatible alphabets: %s , %s (defacto)"% (
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
# 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 = na.zeros( (rows,cols) , dtype=na.float64)
for r in range( rows) :
for c in range(cols):
matrix[r,c] = float( items[r][c])
if position_header :
matrix.transpose()
return Motif(defacto_alphabet, matrix).reindex(alphabet)
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
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!")
# 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))
# 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))
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))
r.pop(0)
defacto_alphabet = ''.join(header)
else:
a = []
for i, r in enumerate(items):
if not ischar(r[0]) and r[0][0] != 'P':
raise ValueError("Expected position "
"as first item on line {}".format(i))
a.append(r.pop(0))
defacto_alphabet = ''.join(a)
# 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
# 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 = na.zeros((rows, cols), dtype=na.float64)
for r in range(rows):
for c in range(cols):
matrix[r, c] = float(items[r][c])
if position_header:
matrix.transpose()
return Motif(defacto_alphabet, matrix).reindex(alphabet)
def read_transfac(fin, alphabet=None):
""" Parse a sequence matrix from a file.
Returns a tuple of (alphabet, matrix)
"""
items = []
start = True
for line in fin:
if line.isspace() or line[0] == '#':
continue
stuff = line.split()
if start and stuff[0] != 'PO' and stuff[0] != 'P0':
continue
if stuff[0] == 'XX' or stuff[0] == '//':
break
start = False
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!")
# 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 %d: " % i)
# Vertical or horizontal arrangement?
if header[0] == 'PO' or header[0] == 'P0':
header.pop(0)
position_header = True
alphabet_header = True
for h in header:
if not isint(h):
position_header = False
if not str.isalpha(h):
alphabet_header = False
if not position_header and not alphabet_header:
raise ValueError("Can't parse header: %s" % str(header))
if position_header and alphabet_header:
raise ValueError("Can't parse header")
# 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 %d" % i)
r.pop(0)
defacto_alphabet = ''.join(header)
else:
a = []
for i, r in enumerate(items):
if not ischar(r[0]) and r[0][0] != 'P':
raise ValueError(
"Expected position as first item on line %d" % i)
a.append(r.pop(0))
defacto_alphabet = ''.join(a)
# Check defacto_alphabet
defacto_alphabet = Alphabet(defacto_alphabet)
if alphabet:
if not defacto_alphabet.alphabetic(alphabet):
raise ValueError("Incompatible alphabets: %s , %s (defacto)" %
(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
# 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 = na.zeros((rows, cols), dtype=na.float64)
for r in range(rows):
for c in range(cols):
matrix[r, c] = float(items[r][c])
if position_header:
matrix.transpose()
return Motif(defacto_alphabet, matrix).reindex(alphabet)
def read_swissRegulon( fin, alphabet=None ):
"""
"""
import re
items = []
start=True
for line in fin :
if line.isspace() or line[0] =='#' or re.search('^//$', line): continue
stuff = line.split()
if start and stuff[0] != 'P0' and stuff[0] != 'PO' : continue
start = False
items.append(stuff[0:5])
if len(items) < 2 :
raise ValueError("Vacuous file.")
# Is the first line a header line?
header = items.pop(0)[0:5]
hcols = len(header)
rows = len(items)
cols = len(items[0])
if not( header[0] =='P0' or header[0] =='PO' or hcols == cols-1 or hcols == cols-2) :
raise ValueError("Missing header line!")
# 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 %d: " % i)
# Vertical or horizontal arrangement?
if header[0] == 'PO' or header[0] == 'P0': header.pop(0)
position_header = True
alphabet_header = True
for h in header :
if not isint(h) : position_header = False
if not str.isalpha(h) : alphabet_header = False
if not position_header and not alphabet_header :
raise ValueError("Can't parse header: %s" % str(header))
if position_header and alphabet_header :
raise ValueError("Can't parse header")
# 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 %d" % i)
r.pop(0)
defacto_alphabet = ''.join(header)
# Check defacto_alphabet
defacto_alphabet = Alphabet(defacto_alphabet)
if alphabet :
if not defacto_alphabet.alphabetic(alphabet) :
raise ValueError("Incompatible alphabets: %s , %s (defacto)"
% (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
# items should now be a list of lists of numbers (as strings)
rows = len(items)
cols = len(items[0])
matrix = na.zeros( (rows,cols) , dtype=na.float64)
for r in range( rows) :
for c in range(cols):
matrix[r,c] = float( items[r][c])
if position_header :
matrix.transpose()
return Motif(defacto_alphabet, matrix).reindex(alphabet)
