# Main args
parser.add_argument("file", type=pathlib.Path,
help="A genome file in .sam format")
parser.add_argument("genome_length", type=int, help="The genome length")
# Options
parser.add_argument("--verbose", default=False, dest="verbose", action="store_true", help="Verbose output")
# Get args
args = parser.parse_args()
input_file = args.file
genome_length = args.genome_length
verbose = args.verbose
# Set loggin level
logging.basicConfig(level=(logging.DEBUG if verbose else None))
logging.debug(f"input_file = {input_file}")
logging.debug(f"genome_length = {genome_length}")
# Read mates
mates = read_mates(input_file, keep_fields=["pos", "ma"])
# Get multiple aligment track
multiple_alignments = get_multiple_alignments(mates, genome_length)
# Print track to wig file
to_wig(multiple_alignments)
if __name__ == "__main__":
# Set verbose logging
logging.basicConfig(level=logging.DEBUG)
# Check args
if len(sys.argv) != 1 + 2:
print_usage(sys.argv)
# Get args
input_file = sys.argv[1]
genome_length = int(sys.argv[2])
logging.debug(f"input_file = {input_file}")
logging.debug(f"genome_length = {genome_length}")
# Read mates
mates = read_mates(input_file,
keep_fields=["pos", "pnext", "tlen", "flag"])
mates = filter_out_invalid_mates(mates)
# Compute single mates percentage
relative_orientations = get_relative_orientations(mates, genome_length)
assert len(
relative_orientations
) == genome_length, f"Track length must be equal to genome lenth, but {len(relative_orientations)} != {genome_length}"
# Print single_mates_percentage in wig format
to_wig(relative_orientations)
""")
# Main args
parser.add_argument("file", type=pathlib.Path, help="A genome file in .sam format")
parser.add_argument("genome_length", type=int, help="The genome length")
# Options
parser.add_argument("--verbose", default=False, dest="verbose", action="store_true", help="Verbose output")
# Get args
args = parser.parse_args()
input_file = args.file
genome_length = args.genome_length
verbose = args.verbose
# Set loggin level
logging.basicConfig(level=(logging.DEBUG if verbose else None))
logging.debug(f"input_file = {input_file}")
logging.debug(f"genome_length = {genome_length}")
# Read mates
mates = read_mates(input_file, keep_fields=["pos", "flag", "cigar"])
# Get multiple aligment track
hard_soft_clippings = get_hard_soft_clippings(mates, genome_length)
# Print track to wig file
to_wig(hard_soft_clippings)
if __name__ == "__main__":
# Set verbose logging
logging.basicConfig(level=logging.DEBUG)
# Check args
if len(sys.argv) != 1 + 2:
print_usage(sys.argv)
# Get args
input_file = sys.argv[1]
genome_length = int(sys.argv[2])
logging.debug(f"input_file = {input_file}")
logging.debug(f"genome_length = {genome_length}")
# Read mates
mates = read_mates(input_file,
keep_fields=["pos", "pnext", "tlen", "flag"])
mates = filter_out_invalid_mates(mates)
# Compute single mates percentage
single_mates_percentage = get_single_mates_percentage(mates, genome_length)
assert len(
single_mates_percentage
) == genome_length, f"Track length must be equal to genome lenth, but {len(single_mates_percentage)} != {genome_length}"
# Print single_mates_percentage in wig format
to_wig(single_mates_percentage)
# Get tlen distribution params
mu, std = get_tlen_distribution_params(mates)
# Plot distribution
if plot:
x = get_distribution_space(mu, std)
prob_insertion = get_probability_for_insertion(x, mu, std)
prob_deletion = get_probability_for_deletion(x, mu, std)
pdf = get_pdf(x, mu, std)
plot_pdf(x, pdf, mu, std)
plot_insertion_probability(x, prob_insertion)
plot_deletion_probability(x, prob_deletion)
if track == "insertion":
logging.info("Computing insertion probabilities...")
ls = get_avg_fragments_length(mates, genome_length)
ls = get_probability_for_insertion(ls, mu, std)
to_wig(ls)
if track == "deletion":
logging.info("Computing deletion probabilities...")
ls = get_avg_fragments_length(mates, genome_length)
ls = get_probability_for_deletion(ls, mu, std)
to_wig(ls)
# Set verbose logging
logging.basicConfig(level=logging.DEBUG)
# Check args
if len(sys.argv) != 1 + 2:
print_usage()
exit(1)
# Get args
input_file = sys.argv[1]
genome_length = int(sys.argv[2])
logging.debug(f"input_file = {input_file}")
logging.debug(f"genome_length = {genome_length}")
# Get mates
mates = read_mates(input_file,
keep_fields=["pos", "pnext", "flag", "tlen"])
mates = filter_out_invalid_mates(mates)
# Compute physical coverage
physical_coverage_percentage = get_physical_coverage_percentage(
mates, genome_length)
assert len(
physical_coverage_percentage
) == genome_length, f"Track length must be equal to genome lenth, but {len(physical_coverage_percentage)} != {genome_length}"
# Print to wig file
to_wig(physical_coverage_percentage)
avg_fragments_length[i] = int(result)
return avg_fragments_length
if __name__ == "__main__":
# Set verbose logging
logging.basicConfig(level=logging.DEBUG)
# Check args
if len(sys.argv) != 1 + 2:
print_usage(sys.argv)
# Get args
input_file = sys.argv[1]
genome_length = int(sys.argv[2])
logging.debug(f"input_file = {input_file}")
logging.debug(f"genome_length = {genome_length}")
# Read mates
mates = read_mates(input_file,
keep_fields=["pos", "pnext", "tlen", "flag"])
mates = filter_out_invalid_mates(mates)
# Compute avg frag length
avg_fragments_length = get_avg_fragments_length(mates, genome_length)
# Print single_mates_percentage in wig format
to_wig(avg_fragments_length)