def parse(self):
# Initial variables #
fields = []
info = {}
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict([p.split('=',1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error("The track%s seems to have an invalid <track> header line", self.path, number)
fields = []
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
# Chromosome #
chrom = items.pop(0)
# Length is nine #
if len(items) != 8:
self.handler.error("The track%s doesn't have nine columns", self.path, number)
# Have we started a track already ? #
if not fields:
self.handler.newTrack(info, self.name)
fields = all_fields[0:len(items)]
self.handler.defineFields(fields)
# Source field #
if items[0] == '.': items[0] = ''
# Name field #
if items[1] == '.': items[1] = ''
# Start and end fields #
try:
items[2] = int(items[2])
items[3] = int(items[3])
except ValueError:
self.handler.error("The track%s has non integers as interval bounds", self.path, number)
if items[3] <= items[2]:
self.handler.error("The track%s has negative or null intervals", self.path, number)
# Score field #
if items[4] == '.' or items[4] == '': items[4] = 0.0
try:
items[4] = float(items[4])
except ValueError:
self.handler.error("The track%s has non floats as score values", self.path, number)
# Strand field #
items[5] = strand_to_int(items[5])
# Frame field #
if items[6] == '.': items[6] = None
else:
try:
items[6] = int(items[6])
except ValueError:
self.handler.error("The track%s has non integers as frame value", self.path, number)
# Group or attribute field #
if items[7] == '.': items[7] = ''
# Yield it #
self.handler.newFeature(chrom, items)
def parse(self):
# Initial variables #
l_chrom, l_name, l_start, l_end, l_strand, l_score = None, None, None, None, None, None
# Start a new track #
self.handler.newTrack({'int_to_float':'score'}, self.name)
self.handler.defineFields(all_fields)
# Line loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
if line.startswith("track "): continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
# Is it a legal line ? #
if len(items) < 5: self.handler.error("The track%s has less than five columns", self.path, number)
# Chromosome #
chrom = items.pop(0)
# Name field #
name = items[0]
# Start and end field #
try: pos = int(items[1])
except ValueError: self.handler.error("The track%s has non integers as position", self.path, number)
start = pos-1
end = pos
# Strand field #
strand = strand_to_int(items[2])
# Score field #
try: score = int(items[3])
except ValueError: self.handler.error("The track%s has non integers as tag count values", self.path, number)
# Ignore null scores #
if score == 0: continue
# Merge adjacent features with same scores #
if (l_chrom, l_name, l_strand, l_score) == (chrom, name, strand, score) and start == l_end:
l_end = end
continue
else:
if l_chrom: self.handler.newFeature(l_chrom, (l_name, l_start, l_end, l_strand, l_score))
l_chrom, l_name, l_start, l_end, l_strand, l_score = chrom, name, start, end, strand, score
# Last feature #
if l_chrom: self.handler.newFeature(l_chrom, (l_name, l_start, l_end, l_strand, l_score))
def parse(self):
# Initial variables #
self.handler.newTrack({'int_to_float':'score'}, self.name)
self.handler.defineFields(all_fields)
with open(self.path) as f:
for number, line in enumerate(f):
items = line.split('\t')
chrom = items.pop(0)
if len(items) < 4: self.handler.error("The track%s doesn't have five columns", self.path, number)
# Name field #
name = items[0]
# Start field #
try: pos = int(items[1])
except ValueError: self.handler.error("The track%s has non integers as position", self.path, number)
# Strand field #
strand = strand_to_int(items[2])
# Score field #
try: score = int(items[3])
except ValueError: self.handler.error("The track%s has non integers as tag count values", self.path, number)
# Yield it #
self.handler.newFeature(chrom, (name, pos-1, pos, strand, score))
def parse(self):
# Initial variables #
info = {}
declare_track = True
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict(
[p.split('=', 1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error(
"The track%s seems to have an invalid <track> header line",
self.path, number)
declare_track = True
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
if len(items) > 8: items = items[0:8] + [' '.join(items[8:])]
# Chromosome #
chrom = items.pop(0)
# Length is nine #
if len(items) != 8:
self.handler.error("The track%s doesn't have nine columns",
self.path, number)
# Have we started a track already ? #
if declare_track:
declare_track = False
self.handler.newTrack(info, self.name)
# Source field #
if items[0] == '.': items[0] = ''
# Name field #
if items[1] == '.': items[1] = ''
# Start and end fields #
try:
items[2] = int(items[2])
items[3] = int(items[3])
except ValueError:
self.handler.error(
"The track%s has non integers as interval bounds",
self.path, number)
# Strand field #
items[5] = strand_to_int(items[5])
# Frame field #
if items[6] == '.': items[6] = None
else:
try:
items[6] = int(items[6])
except ValueError:
self.handler.error(
"The track%s has non integers as frame value",
self.path, number)
# The last special column #
attr = shlex.split(items.pop())
attr = [(attr[i], attr[i + 1].strip(';'))
for i in xrange(0, len(attr), 2)]
# Not using dict to preserve annotation order #
keys, values = [x[0] for x in attr], [x[1] for x in attr]
# GTF attribute column must have annotations starting with "gene_id" and "transcript_id" #
assert ["gene_id", "transcript_id"] == keys[:2], "Invalid " \
"attribute column: %r. Valid attributes begin with " \
"\"gene_id\" and \"transcript_id\""
self.handler.defineFields(all_fields + keys)
items += values
# Yield it #
self.handler.newFeature(chrom, items)
def parse(self):
# Initial variables #
fields = []
info = {}
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict(
[p.split('=', 1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error(
"The track%s seems to have an invalid <track> header line",
self.path, number)
fields = []
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
# Chromosome #
chrom = items.pop(0)
# Length is nine #
if len(items) != 8:
self.handler.error("The track%s doesn't have nine columns",
self.path, number)
# Have we started a track already ? #
if not fields:
self.handler.newTrack(info, self.name)
fields = all_fields[0:len(items)]
self.handler.defineFields(fields)
# Source field #
if items[0] == '.': items[0] = ''
# Name field #
if items[1] == '.': items[1] = ''
# Start and end fields #
try:
items[2] = int(items[2])
items[3] = int(items[3])
except ValueError:
self.handler.error(
"The track%s has non integers as interval bounds",
self.path, number)
if items[3] <= items[2]:
self.handler.error(
"The track%s has negative or null intervals", self.path,
number)
# Score field #
if items[4] == '.' or items[4] == '': items[4] = 0.0
try:
items[4] = float(items[4])
except ValueError:
self.handler.error(
"The track%s has non floats as score values", self.path,
number)
# Strand field #
items[5] = strand_to_int(items[5])
# Frame field #
if items[6] == '.': items[6] = None
else:
try:
items[6] = int(items[6])
except ValueError:
self.handler.error(
"The track%s has non integers as frame value",
self.path, number)
# Group or attribute field #
if items[7] == '.': items[7] = ''
# Yield it #
self.handler.newFeature(chrom, items)
def parse(self):
# Initial variables #
info = {}
declare_track = True
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict([p.split('=',1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error("The track%s seems to have an invalid <track> header line", self.path, number)
declare_track = True
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
if len(items) > 8: items = items[0:8] + [' '.join(items[8:])]
# Chromosome #
chrom = items.pop(0)
# Length is nine #
if len(items) != 8:
self.handler.error("The track%s doesn't have nine columns", self.path, number)
# Have we started a track already ? #
if declare_track:
declare_track = False
self.handler.newTrack(info, self.name)
# Source field #
if items[0] == '.': items[0] = ''
# Name field #
if items[1] == '.': items[1] = ''
# Start and end fields #
try:
items[2] = int(items[2])
items[3] = int(items[3])
except ValueError:
self.handler.error("The track%s has non integers as interval bounds", self.path, number)
# Strand field #
items[5] = strand_to_int(items[5])
# Frame field #
if items[6] == '.': items[6] = None
else:
try:
items[6] = int(items[6])
except ValueError:
self.handler.error("The track%s has non integers as frame value", self.path, number)
# The last special column #
attr = shlex.split(items.pop())
attr = [(attr[i],attr[i+1].strip(';')) for i in xrange(0,len(attr),2)]
# Not using dict to preserve annotation order #
keys, values = [x[0] for x in attr], [x[1] for x in attr]
# GTF attribute column must have annotations starting with "gene_id" and "transcript_id" #
assert ["gene_id", "transcript_id"] == keys[:2], "Invalid " \
"attribute column: %r. Valid attributes begin with " \
"\"gene_id\" and \"transcript_id\""
self.handler.defineFields(all_fields + keys)
items += values
# Yield it #
self.handler.newFeature(chrom, items)
def parse(self):
# Initial variables #
fields = []
info = {}
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict([p.split('=',1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error("The track%s seems to have an invalid <track> header line", self.path, number)
fields = []
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
# Chromosome #
chrom = items.pop(0)
# Have we started a track already ? #
if not fields:
self.handler.newTrack(info, self.name)
fields = all_fields[0:len(items)]
self.handler.defineFields(fields)
# Start and end fields #
try:
items[0] = int(items[0])
items[1] = int(items[1])
except ValueError:
self.handler.error("The track%s has non integers as interval bounds", self.path, number)
except IndexError:
self.handler.error("The track%s has less than two columns", self.path, number)
# All following fields are optional #
try:
# Name field #
if items[2] == '.': items[2] = ''
# Score field #
if items[3] == '.' or items[3] == '': items[3] = 0.0
try:
items[3] = float(items[3])
except ValueError:
self.handler.error("The track%s has non floats as score values", self.path, number)
# Strand field #
items[4] = strand_to_int(items[4])
# Thick starts #
try:
items[5] = float(items[5])
except ValueError:
self.handler.error("The track%s has non integers as thick starts", self.path, number)
# Thick ends #
try:
items[6] = float(items[6])
except ValueError:
self.handler.error("The track%s has non integers as thick ends", self.path, number)
# Too many fields #
if len(items) > 11:
self.handler.error("The track%s has more than twelve columns", self.path, number)
# All index errors are ignored since the fields above three are optional #
except IndexError:
pass
finally:
self.handler.newFeature(chrom, items)
def parse(self):
# Initial variables #
info = {}
declare_track = True
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict(
[p.split('=', 1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error(
"The track%s seems to have an invalid <track> header line",
self.path, number)
declare_track = True
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
if len(items) > 8: items = items[0:8] + [' '.join(items[8:])]
# Chromosome #
chrom = items.pop(0)
# Length is nine #
if len(items) != 8:
self.handler.error("The track%s doesn't have nine columns",
self.path, number)
# Have we started a track already ? #
if declare_track:
declare_track = False
self.handler.newTrack(info, self.name)
# Source field #
if items[0] == '.': items[0] = ''
# Name field #
if items[1] == '.': items[1] = ''
# Start and end fields #
try:
items[2] = int(items[2])
items[3] = int(items[3])
except ValueError:
self.handler.error(
"The track%s has non integers as interval bounds",
self.path, number)
# Score field #
if items[4] == '.' or items[4] == '': items[4] = 0.0
try:
items[4] = float(items[4])
except ValueError:
self.handler.error(
"The track%s has non floats as score values", self.path,
number)
# Strand field #
items[5] = strand_to_int(items[5])
# Frame field #
if items[6] == '.': items[6] = None
else:
try:
items[6] = int(items[6])
except ValueError:
self.handler.error(
"The track%s has non integers as frame value",
self.path, number)
# The last special column #
attr = shlex.split(items.pop())
attr = dict([(attr[i], attr[i + 1].strip(';'))
for i in xrange(0, len(attr), 2)])
self.handler.defineFields(all_fields + attr.keys())
items += attr.values()
# Yield it #
self.handler.newFeature(chrom, items)
def parse(self):
# Initial variables #
info = {}
declare_track = True
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict([p.split('=',1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error("The track%s seems to have an invalid <track> header line", self.path, number)
declare_track = True
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
if len(items) > 8: items = items[0:8] + [' '.join(items[8:])]
# Chromosome #
chrom = items.pop(0)
# Length is nine #
if len(items) != 8:
self.handler.error("The track%s doesn't have nine columns", self.path, number)
# Have we started a track already ? #
if declare_track:
declare_track = False
self.handler.newTrack(info, self.name)
# Source field #
if items[0] == '.': items[0] = ''
# Name field #
if items[1] == '.': items[1] = ''
# Start and end fields #
try:
items[2] = int(items[2])
items[3] = int(items[3])
except ValueError:
self.handler.error("The track%s has non integers as interval bounds", self.path, number)
# Score field #
if items[4] == '.' or items[4] == '': items[4] = 0.0
try:
items[4] = float(items[4])
except ValueError:
self.handler.error("The track%s has non floats as score values", self.path, number)
# Strand field #
items[5] = strand_to_int(items[5])
# Frame field #
if items[6] == '.': items[6] = None
else:
try:
items[6] = int(items[6])
except ValueError:
self.handler.error("The track%s has non integers as frame value", self.path, number)
# The last special column #
attr = shlex.split(items.pop())
attr = dict([(attr[i],attr[i+1].strip(';')) for i in xrange(0,len(attr),2)])
self.handler.defineFields(all_fields + attr.keys())
items += attr.values()
# Yield it #
self.handler.newFeature(chrom, items)
def parse(self):
# Initial variables #
fields = []
info = {}
# Main loop #
for number, line in iterate_lines(self.path):
# Ignored lines #
if line.startswith("browser "): continue
# Track headers #
if line.startswith("track "):
try:
info = dict(
[p.split('=', 1) for p in shlex.split(line[6:])])
except ValueError:
self.handler.error(
"The track%s seems to have an invalid <track> header line",
self.path, number)
fields = []
continue
# Split the lines #
items = line.split('\t')
if len(items) == 1: items = line.split()
# Chromosome #
chrom = items.pop(0)
# Have we started a track already ? #
if not fields:
self.handler.newTrack(info, self.name)
fields = all_fields[0:len(items)]
self.handler.defineFields(fields)
# Start and end fields #
try:
items[0] = int(items[0])
items[1] = int(items[1])
except ValueError:
self.handler.error(
"The track%s has non integers as interval bounds",
self.path, number)
except IndexError:
self.handler.error("The track%s has less than two columns",
self.path, number)
# All following fields are optional #
try:
# Name field #
if items[2] == '.': items[2] = ''
# Score field #
if items[3] == '.' or items[3] == '': items[3] = 0.0
try:
items[3] = float(items[3])
except ValueError:
self.handler.error(
"The track%s has non floats as score values",
self.path, number)
# Strand field #
items[4] = strand_to_int(items[4])
# Thick starts #
try:
items[5] = float(items[5])
except ValueError:
self.handler.error(
"The track%s has non integers as thick starts",
self.path, number)
# Thick ends #
try:
items[6] = float(items[6])
except ValueError:
self.handler.error(
"The track%s has non integers as thick ends",
self.path, number)
# Too many fields #
if len(items) > 11:
self.handler.error(
"The track%s has more than twelve columns", self.path,
number)
# All index errors are ignored since the fields above three are optional #
except IndexError:
pass
finally:
self.handler.newFeature(chrom, items)
