def overlapping_reads(reads, distance):
"""returns all the overlapping reads within a given distance"""
reads_list = []
cur_tss = 0
cur_chrom = ''
for read in reads:
if not cur_tss:
cur_tss = bed12.get_tss(read)
reads_list.append(read)
cur_chrom = bed12.get_chrom(read)
continue
tss = bed12.get_tss(read)
chrom = bed12.get_chrom(read)
#if not overlap
if (tss - cur_tss > distance) or (chrom != cur_chrom):
yield reads_list
reads_list = [read]
cur_tss = tss
cur_chrom = chrom
else:
reads_list.append(read)
cur_tss = tss
yield reads_list
def overlapping_reads(reads, distance):
"""returns all the overlapping reads within a given distance"""
reads_list = []
cur_tss = 0
cur_chrom = ''
for read in reads:
if not cur_tss:
cur_tss = bed12.get_tss(read)
reads_list.append(read)
cur_chrom = bed12.get_chrom(read)
continue
tss = bed12.get_tss(read)
chrom = bed12.get_chrom(read)
#if not overlap
if (tss - cur_tss > distance) or (chrom != cur_chrom):
yield reads_list
reads_list = [read]
cur_tss = tss
cur_chrom = chrom
else:
reads_list.append(read)
cur_tss = tss
yield reads_list
def print_read_to_bed12(reads):
""" Merge the reads by blocks and print a single read in the BED12 format on stdout.
It assumes that the reads are on the same TSS and contains
fingerprint information in the read's name.
Args:
reads: A list of reads
"""
block_sizes, block_starts = bed12.merge_overlapping_blocks(reads)
#bed12
first_read = sorted(reads, key=bed12.get_start)[0]
chrom = bed12.get_chrom(first_read)
start = bed12.get_start(first_read)
end = start + block_starts[-1] + block_sizes[-1]
score = len(reads)
strand = bed12.get_strand(first_read)
if strand == '+':
thick_start = start
thick_end = start + block_sizes[0]
else:
thick_start = end - block_sizes[-1]
thick_end = end
color = "255,0,0"
block_count = len(block_sizes)
block_sizes = ','.join(map(str, block_sizes))
block_starts = ','.join(map(str, block_starts))
name = map(str, [chrom, start, end, strand])
name = ":".join(name)
output = [
chrom, start, end, name, score, strand, thick_start, thick_end, color,
block_count, block_sizes, block_starts
]
output_str = map(str, output)
print '\t'.join(output_str)
def print_read_to_bed12(reads):
""" Merge the reads by blocks and print a single read in the BED12 format on stdout.
It assumes that the reads are on the same TSS and contains
fingerprint information in the read's name.
Args:
reads: A list of reads
"""
block_sizes, block_starts = bed12.merge_overlapping_blocks(reads)
#bed12
first_read = sorted(reads, key=bed12.get_start)[0]
chrom = bed12.get_chrom(first_read)
start = bed12.get_start(first_read)
end = start + block_starts[-1] + block_sizes[-1]
score = len(reads)
strand = bed12.get_strand(first_read)
if strand == '+':
thick_start = start
thick_end = start + block_sizes[0]
else:
thick_start = end - block_sizes[-1]
thick_end = end
color = "255,0,0"
block_count = len(block_sizes)
block_sizes = ','.join(map(str, block_sizes))
block_starts = ','.join(map(str, block_starts))
name = map(str, [chrom, start, end, strand])
name = ":".join(name)
output = [chrom, start, end, name, score, strand, thick_start, thick_end,
color, block_count, block_sizes, block_starts]
output_str = map(str, output)
print '\t'.join(output_str)
def main():
#PARSER TODO: move this code somewhere else
parser = argparse.ArgumentParser()
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument(
"-d",
"--directory",
help="absolute path of the folder containing the bed files")
group.add_argument("-f", "--file", help="a bed file")
parser.add_argument(
"-o",
help=
'name of the output file. Only works if the script is called with the -f option, \
ignored otherwise.')
args = parser.parse_args()
if args.directory:
path, folder, files = os.walk(args.directory).next()
elif args.file:
path = ''
files = [args.file]
#ENDPARSER
#create a temporary directory
tmp_dir = tempfile.mkdtemp()
plus_strand_tmp_file = open(os.path.join(tmp_dir, '+'), 'w')
minus_strand_tmp_file = open(os.path.join(tmp_dir, '-'), 'w')
plus_and_minus_sorted_path = os.path.join(tmp_dir, '+-s')
#creates two temporary bed files containing either reads on the plus or minus strand
for bed_file in files:
with open(os.path.join(path, bed_file)) as bed_file:
reader = csv.reader(bed_file, delimiter='\t')
for read in reader:
strand = bed12.get_strand(read)
if strand == '+':
plus_strand_tmp_file.write('\t'.join(read) + '\n')
elif strand == '-':
minus_strand_tmp_file.write('\t'.join(read) + '\n')
#close the files
plus_strand_tmp_file.close()
minus_strand_tmp_file.close()
#call unix sort on the file containing reads on the plus strand by tss
with open(os.path.join(tmp_dir, '+sorted'), "w") as outfile:
subprocess.call(
["sort", '-k1,1', '-k2,2n',
os.path.join(tmp_dir, '+')],
stdout=outfile)
#call unix sort on the file containing reads on the minus strand by tss
with open(os.path.join(tmp_dir, '-sorted'), "w") as outfile:
subprocess.call(
["sort", '-k1,1', '-k3,3n',
os.path.join(tmp_dir, '-')],
stdout=outfile)
#concatenate the files sorted by tss
with open(plus_and_minus_sorted_path, "w") as outfile:
subprocess.call([
'cat',
os.path.join(tmp_dir, '+sorted'),
os.path.join(tmp_dir, '-sorted')
],
stdout=outfile)
with open(plus_and_minus_sorted_path) as bedfile:
reader = csv.reader(bedfile, delimiter='\t')
reads = (line for line in reader)
#for each reads on the same tss
for tss, same_tss_reads in itertools.groupby(reads, bed12.get_tss):
d = defaultdict(list)
#group the reads by chr and fingerprint
for read in same_tss_reads:
key = (bed12.get_chrom(read), get_fingerprint(read))
d[key].append(read)
#merge and print the reads that have same tss, and fingerprint
for key, same_fingerprint_reads in d.iteritems():
print_read_to_bed12(key, same_fingerprint_reads)
shutil.rmtree(tmp_dir)
def main():
# PARSER TODO: move this code somewhere else
parser = argparse.ArgumentParser()
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument("-d", "--directory", help="absolute path of the folder containing the bed files")
group.add_argument("-f", "--file", help="a bed file")
parser.add_argument(
"-o",
help="name of the output file. Only works if the script is called with the -f option, \
ignored otherwise.",
)
args = parser.parse_args()
if args.directory:
path, folder, files = os.walk(args.directory).next()
elif args.file:
path = ""
files = [args.file]
# ENDPARSER
# create a temporary directory
tmp_dir = tempfile.mkdtemp()
plus_strand_tmp_file = open(os.path.join(tmp_dir, "+"), "w")
minus_strand_tmp_file = open(os.path.join(tmp_dir, "-"), "w")
plus_and_minus_sorted_path = os.path.join(tmp_dir, "+-s")
# creates two temporary bed files containing either reads on the plus or minus strand
for bed_file in files:
with open(os.path.join(path, bed_file)) as bed_file:
reader = csv.reader(bed_file, delimiter="\t")
for read in reader:
strand = bed12.get_strand(read)
if strand == "+":
plus_strand_tmp_file.write("\t".join(read) + "\n")
elif strand == "-":
minus_strand_tmp_file.write("\t".join(read) + "\n")
# close the files
plus_strand_tmp_file.close()
minus_strand_tmp_file.close()
# call unix sort on the file containing reads on the plus strand by tss
with open(os.path.join(tmp_dir, "+sorted"), "w") as outfile:
subprocess.call(["sort", "-k2,2n", os.path.join(tmp_dir, "+")], stdout=outfile)
# call unix sort on the file containing reads on the minus strand by tss
with open(os.path.join(tmp_dir, "-sorted"), "w") as outfile:
subprocess.call(["sort", "-k3,3n", os.path.join(tmp_dir, "-")], stdout=outfile)
# concatenate the files sorted by tss
with open(plus_and_minus_sorted_path, "w") as outfile:
subprocess.call(["cat", os.path.join(tmp_dir, "+sorted"), os.path.join(tmp_dir, "-sorted")], stdout=outfile)
with open(plus_and_minus_sorted_path) as bedfile:
reader = csv.reader(bedfile, delimiter="\t")
reads = (line for line in reader)
# for each reads on the same tss
for tss, reads in itertools.groupby(reads, bed12.get_tss):
d = defaultdict(list)
# group the reads by chr, barcode and fingerprint
for read in reads:
key = (bed12.get_chrom(read), get_barcode(read), get_fingerprint(read))
d[key].append(read)
# merge and print the reads that have similar tss, barcode and fingerprint
for key, reads in d.iteritems():
print_read_to_bed12(key, reads)
shutil.rmtree(tmp_dir)