def main():
args = getArgs()
samples = args.i
output = args.o
chr = args.c
ncpu = args.p
resolution = args.r
species = args.s
gbuild = args.b
# initiate a chromosome object that will store all Hi-C data and analysis
my_chrom = Chromosome(
name=chr, # 染色体名
centromere_search=True, # centromereを検出するか
species=species,
assembly=gbuild # genome build
)
for sample in samples:
label, path = sample.split(",")
print(label)
print(path)
getHiCData(my_chrom, output, label, path, resolution, ncpu)
# if not os.path.exists('tdb'):
# os.makedirs("tdb")
my_chrom.save_chromosome(output + ".tdb", force=True)
def test_05_save_load(self):
test_chr = Chromosome(name='Test Chromosome',
experiment_tads=[exp1, exp2],
experiment_names=['exp1', 'exp2'],
experiment_resolutions=[20000,20000])
test_chr.save_chromosome('lolo', force=True)
test_chr = load_chromosome('lolo')
system('rm -f lolo')
system('rm -f lolo_hic')
def test_05_save_load(self):
if CHKTIME:
t0 = time()
test_chr1 = Chromosome(name='Test Chromosome',
experiment_tads=[exp1, exp2],
experiment_names=['exp1', 'exp2'],
experiment_resolutions=[20000, 20000],
silent=True)
test_chr1.save_chromosome('lolo', force=True)
test_chr2 = load_chromosome('lolo')
system('rm -f lolo')
system('rm -f lolo_hic')
self.assertEqual(str(test_chr1.__dict__), str(test_chr2.__dict__))
if CHKTIME:
print '5', time() - t0
def test_05_save_load(self):
if CHKTIME:
t0 = time()
test_chr1 = Chromosome(name='Test Chromosome',
experiment_tads=[exp1, exp2],
experiment_names=['exp1', 'exp2'],
experiment_resolutions=[20000,20000],
silent=True)
test_chr1.save_chromosome('lolo', force=True)
test_chr2 = load_chromosome('lolo')
system('rm -f lolo')
system('rm -f lolo_hic')
self.assertEqual(str(test_chr1.__dict__), str(test_chr2.__dict__))
if CHKTIME:
print '5', time() - t0
def test_05_save_load(self):
if ONLY and not "05" in ONLY:
return
if CHKTIME:
t0 = time()
test_chr1 = Chromosome(name="Test Chromosome",
experiment_tads=[exp1, exp2],
experiment_names=["exp1", "exp2"],
experiment_resolutions=[20000, 20000],
silent=True)
test_chr1.save_chromosome("lolo", force=True)
test_chr2 = load_chromosome("lolo")
system("rm -f lolo")
system("rm -f lolo_hic")
self.assertEqual(str(test_chr1.__dict__), str(test_chr2.__dict__))
if CHKTIME:
print "5", time() - t0
def test_05_save_load(self):
if ONLY and ONLY != "05":
return
if CHKTIME:
t0 = time()
test_chr1 = Chromosome(
name="Test Chromosome",
experiment_tads=[exp1, exp2],
experiment_names=["exp1", "exp2"],
experiment_resolutions=[20000, 20000],
silent=True,
)
test_chr1.save_chromosome("lolo", force=True)
test_chr2 = load_chromosome("lolo")
system("rm -f lolo")
system("rm -f lolo_hic")
self.assertEqual(str(test_chr1.__dict__), str(test_chr2.__dict__))
if CHKTIME:
print "5", time() - t0
def process():
if (options.outputFilename != ""):
outfilefileprefix = options.outputDir + options.outputFilename
else:
outfilefileprefix = options.outputDir + os.path.basename(args[0])
for matrixFile in xrange(len(args)):
sample = os.path.splitext(os.path.basename(
args[matrixFile]))[0].split(".matrix")[0]
chr = sample.rsplit(".", 1)[-1]
sample = sample.rsplit(".", 1)[0]
chrom = Chromosome(name=chr,
centromere_search=True,
species=options.species,
assembly=options.assembly)
chrom.set_max_tad_size(5000000)
chrom.add_experiment(sample,
exp_type='Hi-C',
identifier=sample,
hic_data=args[matrixFile],
resolution=options.resolution)
exp = chrom.experiments[sample]
exp.normalize_hic(silent=True)
chrom.find_tad(sample,
n_cpus=options.threads,
normalized=True,
verbose=False)
exp.write_tad_borders(outfilefileprefix + "." + chr + ".border")
# chrom.tad_density_plot(sample,savefig=outfilefileprefix+".density."+chr+".pdf")
chrom.visualize(exp.name,
paint_tads=True,
savefig=outfilefileprefix + "chr." + chr + ".pdf")
chrom.save_chromosome(outfilefileprefix + "chr." + chr + ".tdb",
force=True)
def process():
if ( options.outputFilename != "" ):
outfilefileprefix=options.outputDir+options.outputFilename
else:
outfilefileprefix=options.outputDir+os.path.basename(args[0])
for matrixFile in xrange(len(args)):
sample=os.path.splitext(os.path.basename(args[matrixFile]))[0].split(".matrix")[0]
chr = sample.rsplit(".",1)[-1]
sample = sample.rsplit(".",1)[0]
chrom = Chromosome(name=chr, centromere_search=True, species=options.species, assembly=options.assembly)
chrom.set_max_tad_size(5000000)
chrom.add_experiment(sample, exp_type='Hi-C', identifier=sample,
hic_data=args[matrixFile], resolution=options.resolution)
exp = chrom.experiments[sample]
exp.normalize_hic(silent=True)
chrom.find_tad(sample, n_cpus=options.threads, normalized=True, verbose=False)
exp.write_tad_borders(outfilefileprefix+"."+chr+".border")
# chrom.tad_density_plot(sample,savefig=outfilefileprefix+".density."+chr+".pdf")
chrom.visualize(exp.name, paint_tads=True, savefig=outfilefileprefix+"chr."+chr+".pdf")
chrom.save_chromosome(outfilefileprefix+"chr."+chr+".tdb", force=True)
def call_tads(matrix_filenames, chrom_name):
print
print "Call TADs for chromosome " + chrom_name + '...'
print "Contact matrices: "
for matrix_filename in matrix_filenames:
print matrix_filename
chrom_number = search(r'\d+|X|Y', chrom_name).group(0)
if len(chrom_number) == 1 and chrom_number != 'X' and chrom_number != 'Y':
chrom_number = '0' + chrom_number
chrom_id = 'chr' + chrom_number
else:
chrom_id = chrom_name
output_txt_filename = join(txt_directory, chrom_id + '_TADs.txt')
print 'Output TXT file:', output_txt_filename
output_bed_filename = join(bed_directory, chrom_id + '_TADs.bed')
print 'Output BED file:', output_bed_filename
filename_list.append(output_bed_filename)
"""tads_2D_filename = join(png_directory, chrom_id + '_TADs_2D.png')
print 'Output 2D TAD plot file:', tads_2D_filename
tads_1D_filename = join(png_directory, chrom_id + '_TADs_1D.png')
print 'Output 1D TAD plot file:', tads_1D_filename"""
# Call TADs and write their borders in TADbit text format and in BED format
chrom = Chromosome(name=chrom_name)
if len(matrix_filenames) > 1: # several matrices for one chromosome
combined_experiment_name = 'batch'
experiment_names = []
for matrix_index, matrix_filename in enumerate(matrix_filenames):
experiment_name = splitext(basename(matrix_filename))[0] + '_' + str(matrix_index)
experiment_names.append(experiment_name)
combined_experiment_name += '_' + experiment_name
chrom.add_experiment(experiment_name, hic_data=matrix_filename, \
resolution=matrix_resolution)
chrom.find_tad(experiment_names, batch_mode = True, n_cpus=thread_number)
chrom.experiments[combined_experiment_name].write_tad_borders(savedata=output_txt_filename)
#chrom.visualize(combined_experiment_name, paint_tads=True, savefig=tads_2D_filename)
#chrom.tad_density_plot(combined_experiment_name, savefig=tads_1D_filename)
else: # only one matrix for one chromosome
matrix_filename = matrix_filenames[0]
experiment_name = splitext(basename(matrix_filename))[0]
chrom.add_experiment(experiment_name, hic_data=matrix_filename, \
resolution=matrix_resolution)
chrom.find_tad(experiment_name, n_cpus=thread_number)
chrom.experiments[experiment_name].write_tad_borders(savedata=output_txt_filename)
#chrom.visualize(experiment_name, paint_tads=True, savefig=tads_2D_filename)
#chrom.tad_density_plot(experiment_name, savefig=tads_1D_filename)
with open(output_txt_filename, 'r') as src, open(output_bed_filename, 'w') as dst:
track_line = 'track name="' + chrom_name + '_TADs" visibility=1 itemRgb="On"'
dst.write(track_line + '\n')
for i, line in enumerate(src):
if line.split()[0] == '#':
continue
line_list = line.split()
tad_name = chrom_name + '.' + 'TAD' + '.' + str(i)
# Coordinates in BED format are 0-based,
# and a region is presented by [x,y) interval.
start_pos = (int(line_list[1]) - 1) * matrix_resolution
end_pos = int(line_list[2]) * matrix_resolution
score = 0 # Just to fill in the field
strand = '.' # Just to fill in the field
if i%2:
color = '0,0,255' # blue
else:
color = '255,0,0' # red
bed_line = chrom_name + '\t' + str(start_pos) + '\t' + str(end_pos) + '\t' + \
tad_name + '\t' + str(score) + '\t' + strand + '\t' + \
str(start_pos) + '\t' + str(end_pos) + '\t' + color
dst.write(bed_line + '\n')
chrom_filename = join(tdb_directory, chrom_id + '.tdb')
chrom.save_chromosome(chrom_filename, force=True)
print 'Finish.'
def call_tads(matrix_filenames, chrom_name):
print
print "Call TADs for chromosome " + chrom_name + '...'
print "Contact matrices: "
for matrix_filename in matrix_filenames:
print matrix_filename
chrom_number = search(r'\d+|X|Y', chrom_name).group(0)
if len(chrom_number) == 1 and chrom_number != 'X' and chrom_number != 'Y':
chrom_number = '0' + chrom_number
chrom_id = 'chr' + chrom_number
else:
chrom_id = chrom_name
output_txt_filename = join(txt_directory, chrom_id + '_TADs.txt')
print 'Output TXT file:', output_txt_filename
output_bed_filename = join(bed_directory, chrom_id + '_TADs.bed')
print 'Output BED file:', output_bed_filename
filename_list.append(output_bed_filename)
"""tads_2D_filename = join(png_directory, chrom_id + '_TADs_2D.png')
print 'Output 2D TAD plot file:', tads_2D_filename
tads_1D_filename = join(png_directory, chrom_id + '_TADs_1D.png')
print 'Output 1D TAD plot file:', tads_1D_filename"""
# Call TADs and write their borders in TADbit text format and in BED format
chrom = Chromosome(name=chrom_name)
if len(matrix_filenames) > 1: # several matrices for one chromosome
combined_experiment_name = 'batch'
experiment_names = []
for matrix_index, matrix_filename in enumerate(matrix_filenames):
experiment_name = splitext(
basename(matrix_filename))[0] + '_' + str(matrix_index)
experiment_names.append(experiment_name)
combined_experiment_name += '_' + experiment_name
chrom.add_experiment(experiment_name, hic_data=matrix_filename, \
resolution=matrix_resolution)
chrom.find_tad(experiment_names, batch_mode=True, n_cpus=thread_number)
chrom.experiments[combined_experiment_name].write_tad_borders(
savedata=output_txt_filename)
#chrom.visualize(combined_experiment_name, paint_tads=True, savefig=tads_2D_filename)
#chrom.tad_density_plot(combined_experiment_name, savefig=tads_1D_filename)
else: # only one matrix for one chromosome
matrix_filename = matrix_filenames[0]
experiment_name = splitext(basename(matrix_filename))[0]
chrom.add_experiment(experiment_name, hic_data=matrix_filename, \
resolution=matrix_resolution)
chrom.find_tad(experiment_name, n_cpus=thread_number)
chrom.experiments[experiment_name].write_tad_borders(
savedata=output_txt_filename)
#chrom.visualize(experiment_name, paint_tads=True, savefig=tads_2D_filename)
#chrom.tad_density_plot(experiment_name, savefig=tads_1D_filename)
with open(output_txt_filename, 'r') as src, open(output_bed_filename,
'w') as dst:
track_line = 'track name="' + chrom_name + '_TADs" visibility=1 itemRgb="On"'
dst.write(track_line + '\n')
for i, line in enumerate(src):
if line.split()[0] == '#':
continue
line_list = line.split()
tad_name = chrom_name + '.' + 'TAD' + '.' + str(i)
# Coordinates in BED format are 0-based,
# and a region is presented by [x,y) interval.
start_pos = (int(line_list[1]) - 1) * matrix_resolution
end_pos = int(line_list[2]) * matrix_resolution
score = 0 # Just to fill in the field
strand = '.' # Just to fill in the field
if i % 2:
color = '0,0,255' # blue
else:
color = '255,0,0' # red
bed_line = chrom_name + '\t' + str(start_pos) + '\t' + str(end_pos) + '\t' + \
tad_name + '\t' + str(score) + '\t' + strand + '\t' + \
str(start_pos) + '\t' + str(end_pos) + '\t' + color
dst.write(bed_line + '\n')
chrom_filename = join(tdb_directory, chrom_id + '.tdb')
chrom.save_chromosome(chrom_filename, force=True)
print 'Finish.'