def SW(s1,s2):
"""Return (alignment string, sw score).
sequences are taken as read - no complementing or reversing.
returns ('',-1) if there is no alignment.
Score is an integer using the PAM47 matrix.
"""
if type(s1) != StringType or type(s2) != StringType:
raise AttributeError, "s1 and s2 must be strings"
sizeDiff = len(s1)-len(s2)
if sizeDiff > 0:
s2+='x'*sizeDiff
elif sizeDiff < 0:
s1+='x'*abs(sizeDiff)
s2=sequence.reverse(s2)
sLen = len(s1)
outBuffer = ctypes.create_string_buffer(sLen*5)
__aos.SW(ctypes.c_char_p(s1),
ctypes.c_char_p(s2),
ctypes.c_int(1),
ctypes.c_int(sLen),
outBuffer)
outLines = outBuffer.value.split('\n')
#print outLines
if len(outLines) > 3:
alignment = '\n'.join(outLines[0:2])
score = int(outLines[2])
return (alignment,score)
else:
return ('',-1)
def energy(s1,s2):
"""Return melting energy for association of s1/s2.
"""
if type(s1) != StringType or type(s2) != StringType:
raise AttributeError, "s1 and s2 must be strings"
if len(s2) != len(s1):
raise SequenceLengthError, "s1 and s2 are different lengths."
s2=sequence.reverse(s2)
return __aos.energy(ctypes.c_char_p(s1),ctypes.c_char_p(s2),ctypes.c_int(0))
action="store_true",
dest="complement",
help="Complement sequence",
default=False)
parser.add_option(
"-b", "--reverseComplement", "--revComp",
action="store_true",
dest="reverseComplement",
help="Reverse complement sequence", default=False)
options, args = parser.parse_args(sys.argv)
iFilename = args[1]
start = int(args[2])
end = int(args[3])
header,seq = fasta.load(iFilename)
s = seq[start-1:end]
h = '%s %i-%i' % (header,start,end)
if options.reverse:
s = sequence.reverse(s)
h += '(r)'
elif options.complement:
s = sequence.complement(s)
h += '(c)'
elif options.reverseComplement:
s = sequence.reverse_complement(s)
h += '(rc)'
fasta.pretty(h, s, width=options.width)
help="Complement sequence",
default=False)
parser.add_option("-b",
"--reverseComplement",
"--revComp",
action="store_true",
dest="reverseComplement",
help="Reverse complement sequence",
default=False)
options, args = parser.parse_args(sys.argv)
iFilename = args[1]
start = int(args[2])
end = int(args[3])
header, seq = fasta.load(iFilename)
s = seq[start - 1:end]
h = '%s %i-%i' % (header, start, end)
if options.reverse:
s = sequence.reverse(s)
h += '(r)'
elif options.complement:
s = sequence.complement(s)
h += '(c)'
elif options.reverseComplement:
s = sequence.reverse_complement(s)
h += '(rc)'
fasta.pretty(h, s, width=options.width)