def newFeature(self, chrom, feature):
# Put the fields in the right order #
line = [feature[i] for i in self.indices]
# Convert the score #
line[2] = format_float(line[2])
# Make sure eveything is a string #
line = [str(f) for f in line]
# Write one line #
self.file.write(' '.join([chrom] + line) + '\n')
def newFeature(self, chrom, feature):
# Put the fields in the right order #
line = [feature[i] for i in self.indices]
# Convert the score #
line[2] = format_float(line[2])
# Make sure eveything is a string #
line = [str(f) for f in line]
# Write one line #
self.file.write(' '.join([chrom] + line) + '\n')
def newFeature(self, chrom, feature):
# Put the fields in the right order #
if self.indices: line = [feature[i] if i != None else '' for i in self.indices]
else: line = list(feature)
# Convert the score #
try: line[3] = format_float(line[3])
except IndexError: pass
# Convert the strand #
try: line[4] = int_to_strand(line[4])
except IndexError: pass
# Make sure eveything is a string #
line = [str(f) for f in line]
# Write one line #
self.file.write('\t'.join([chrom] + line) + '\n')
def newFeature(self, chrom, feature):
# Put the fields in the right order #
if self.indices: f = [feature[i] for i in self.indices]
else: f = list(feature)
start, end, span, score = f[0], f[1], f[1]-f[0], format_float(f[2])
# Look ahead #
if not self.previous_end:
self.writeFixedStep(chrom, start, end, span, score)
return
# If we have the same span just add the score #
if start == self.previous_end and span == self.previous_span:
self.file.write(score + '\n')
self.previous_end += span
else:
self.writeFixedStep(chrom, start, end, span, score)
def newFeature(self, chrom, feature):
# Put the fields in the right order #
line = range(len(all_fields))
for n,i in enumerate(self.indices):
if i == -1: line[n] = defaults[n]
else: line[n] = feature[i]
# Convert the score #
line[4] = format_float(line[4])
# Convert the strand #
line[5] = int_to_strand(line[5])
# Convert the frame #
if line[6] == '' or line[6] == None: line[6] = '.'
# Make sure eveything is a string #
line = [str(f) for f in line]
# Write one line #
self.file.write('\t'.join([chrom] + line) + '\n')
def newFeature(self, chrom, feature):
# Put the fields in the right order #
line = range(len(all_fields))
for n,i in enumerate(self.indices):
if i == -1: line[n] = defaults[n]
else: line[n] = feature[i]
# Convert the score #
line[4] = format_float(line[4])
# Convert the strand #
line[5] = int_to_strand(line[5])
# Convert the frame #
if line[6] == '' or line[6] == None: line[6] = '.'
# Make sure eveything is a string #
line = [str(f) for f in line]
# Write one line #
self.file.write('\t'.join([chrom] + line) + '\n')