class Paragraph(object):
def __init__(self,paragraph_lines,ignore_recognizer=False):
self.paragraph_lines = paragraph_lines
self.header = Header(paragraph_lines[0])
#Paragraph can't end with empty line!
seq_lines = [line for line in paragraph_lines[1:]
if line[0] in string.uppercase]
recognizer_lines = [line for line in paragraph_lines[1:]
if not line[0] in string.uppercase]
self.seq_data = map(SequenceData,seq_lines)
if not ignore_recognizer:
recognizer_data = [[float(val) for val in line.split(",")]
for line in recognizer_lines]
else:
recognizer_data = [[0 for i in range(len(self.seq_data[0].site))]
for j in range(4)]
self.recognizer = RecognizerFactory(recognizer_data)
def toFasta(self):
return "\n".join([">Site %s\n%s" % (i,seq.site)
for i,seq in enumerate(self.seq_data)])
def motif(self):
return [seq.site for seq in self.seq_data]
def adjusted_motif(self):
def adjust(site):
if self.recognizer.score(site) < self.recognizer.score(wc(site)):
return site
else:
return wc(site)
return [adjust(site) for site in self.motif()]
def __init__(self,paragraph_lines,ignore_recognizer=False):
self.paragraph_lines = paragraph_lines
self.header = Header(paragraph_lines[0])
#Paragraph can't end with empty line!
seq_lines = [line for line in paragraph_lines[1:]
if line[0] in string.uppercase]
recognizer_lines = [line for line in paragraph_lines[1:]
if not line[0] in string.uppercase]
self.seq_data = map(SequenceData,seq_lines)
if not ignore_recognizer:
recognizer_data = [[float(val) for val in line.split(",")]
for line in recognizer_lines]
else:
recognizer_data = [[0 for i in range(len(self.seq_data[0].site))]
for j in range(4)]
self.recognizer = RecognizerFactory(recognizer_data)
