def print_read_to_bed12(key, 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
barcode and fingerprint information in the read's name.
Args:
key: A tuple that contain the chromosome, barcode and fingerprint information.
reads: A list of reads (in a list) from the same TSS, that have similar barcode and fingerprint.
>>> reads = []
>>> reads.append(['chrX', '100', '200', 'BC:AAA;FP:0012', '12', '+', '100', '110', '255,0,0', '2', '20,25', '0,75'])
>>> reads.append(['chrX', '100', '300', 'BC:AAA;FP:0012', '12', '+', '100', '110', '255,0,0', '3', '20,25', '0,175'])
>>> print_read_to_bed12(('chrX', 'AAA', '0012'), reads) #doctest: +NORMALIZE_WHITESPACE
chrX 100 300 BC:AAA;FP:0012 2 + 100 120 255,0,0 3 20,25,25 0,75,175
"""
block_sizes, block_starts = bed12.merge_overlapping_blocks(reads)
# bed12
first_read = sorted(reads, key=bed12.get_start)[0]
chrom, barcode, fingerprint = key
start = bed12.get_start(first_read)
end = start + block_starts[-1] + block_sizes[-1]
name = "BC:{0};FP:{1}".format(barcode, fingerprint)
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))
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(key, 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:
key: A tuple that contain the chromosome, barcode and fingerprint information.
reads: A list of reads (in a list) from the same TSS, that have similar barcode and fingerprint.
>>> reads = []
>>> reads.append(['chrX', '100', '200', 'FP:0012', '12', '+', '100', '110', '255,0,0', '2', '20,25', '0,75'])
>>> reads.append(['chrX', '100', '300', 'FP:0012', '12', '+', '100', '110', '255,0,0', '3', '20,25', '0,175'])
>>> print_read_to_bed12(('chrX', '0012'), reads) #doctest: +NORMALIZE_WHITESPACE
chrX 100 300 FP:0012 2 + 100 120 255,0,0 3 20,25,25 0,75,175
"""
block_sizes, block_starts = bed12.merge_overlapping_blocks(reads)
#bed12
first_read = sorted(reads, key=bed12.get_start)[0]
chrom, fingerprint = key
start = bed12.get_start(first_read)
end = start + block_starts[-1] + block_sizes[-1]
name = "FP:{0}".format(fingerprint)
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))
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 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)