def write_chip_seq_data(chip_seq_data, filename):
genome = get_ecoli_genome()
with open(filename, 'w') as f:
for (i, (base,
val)) in verbose_gen(enumerate(zip(genome, chip_seq_data)),
10**5):
f.write("%s,%s,%s\n" % (i, base, val))
def interpret_map_file(filename):
chip_seq_data = [0 for _ in get_ecoli_genome()]
lines_so_far = 0
reads = 0
read_length = 51
n = len(get_ecoli_genome())
with open(filename) as f:
for line in f:
lines_so_far += 1
if line.startswith("UB-NGS"):
reads += 1
fields = line.split("\t")
strand = fields[1]
assert strand == "+" or strand == "-"
strand_direction = 1 if strand == "+" else -1
index = int(fields[3])
if reads % 10000 == 0:
print index,lines_so_far/13460000.0
for i in xrange(read_length):
chip_seq_data[(index + i*strand_direction)%n] += 1
return chip_seq_data
def interpret_map_file(filename):
chip_seq_data = [0 for _ in get_ecoli_genome()]
lines_so_far = 0
reads = 0
read_length = 51
n = len(get_ecoli_genome())
with open(filename) as f:
for line in f:
lines_so_far += 1
if line.startswith("UB-NGS"):
reads += 1
fields = line.split("\t")
strand = fields[1]
assert strand == "+" or strand == "-"
strand_direction = 1 if strand == "+" else -1
index = int(fields[3])
if reads % 10000 == 0:
print index, lines_so_far / 13460000.0
for i in xrange(read_length):
chip_seq_data[(index + i * strand_direction) % n] += 1
return chip_seq_data
def write_chip_seq_data(chip_seq_data,filename):
genome = get_ecoli_genome()
with open(filename,'w') as f:
for (i,(base,val)) in verbose_gen(enumerate(zip(genome,chip_seq_data)),10**5):
f.write("%s,%s,%s\n"%(i,base,val))
