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 #
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')
def newFeature(self, chrom, feature):
# function to obtain attribute column key-value string
def attribute_str(key, value):
return '%s "%s";' % (key, value)
# Put the fields in the right order #
# GTF entries always have 8 columns (excluding the seqname column)
line = range(8)
for n, i in enumerate(self.indices):
# i == -1 indicates we should use the default value #
if i == -1:
if n < 7:
# Everything before the attribute column #
line[n] = defaults[n]
elif n == 7:
# "gene_id" annotation #
line[n] = attribute_str(self.fields[n], defaults[n])
elif n == 8:
# "transcript_id annotation #
attr = attribute_str(self.fields[n], defaults[n])
line[7] = '%s %s' % (line[7], attr)
else:
# Annotations of the attribute columns without defaults #
raise ValueError("Default value for the %r attribute "
"column is not defined." % self.fields[n])
else:
if n < 7:
line[n] = feature[i]
elif n == 7:
# "gene_id" annotation #
line[n] = attribute_str(self.fields[n], feature[i])
else:
# Everything after the "gene_id" annotation #
attr = attribute_str(self.fields[n], feature[i])
line[7] = '%s %s' % (line[7], attr)
# Convert end from UCSC back to Ensembl #
line[3] = line[3] - 1
# 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):
# function to obtain attribute column key-value string
def attribute_str(key, value):
return '%s "%s";' % (key, value)
# Put the fields in the right order #
# GTF entries always have 8 columns (excluding the seqname column)
line = range(8)
for n, i in enumerate(self.indices):
# i == -1 indicates we should use the default value #
if i == -1:
if n < 7:
# Everything before the attribute column #
line[n] = defaults[n]
elif n == 7:
# "gene_id" annotation #
line[n] = attribute_str(self.fields[n], defaults[n])
elif n == 8:
# "transcript_id annotation #
attr = attribute_str(self.fields[n], defaults[n])
line[7] = '%s %s' % (line[7], attr)
else:
# Annotations of the attribute columns without defaults #
raise ValueError("Default value for the %r attribute "
"column is not defined." % self.fields[n])
else:
if n < 7:
line[n] = feature[i]
elif n == 7:
# "gene_id" annotation #
line[n] = attribute_str(self.fields[n], feature[i])
else:
# Everything after the "gene_id" annotation #
attr = attribute_str(self.fields[n], feature[i])
line[7] = '%s %s' % (line[7], attr)
# 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')
