def get_sizes(args):
"""function to get fragment sizes
"""
if args.out is None:
args.out = '.'.join(os.path.basename(args.bam).split('.')[0:-1])
sizes = FragmentSizes(lower = args.lower, upper = args.upper, atac = args.atac)
if args.bed:
chunks = ChunkList.read(args.bed)
chunks.merge()
sizes.calculateSizes(args.bam, chunks)
else:
sizes.calculateSizes(args.bam)
sizes.save(args.out+'.fragmentsizes.txt')
if not args.no_plot:
#make figure
fig = plt.figure()
plt.plot(range(sizes.lower,sizes.upper),sizes.get(sizes.lower,sizes.upper),label = args.out)
plt.xlabel("Fragment Size")
plt.ylabel("Frequency")
fig.savefig(args.out+'.fragmentsizes.eps')
plt.close(fig)
def get_sizes(args):
"""function to get fragment sizes
"""
if args.out is None:
args.out = '.'.join(os.path.basename(args.bam).split('.')[0:-1])
sizes = FragmentSizes(lower=args.lower, upper=args.upper, atac=args.atac)
if args.bed:
chunks = ChunkList.read(args.bed)
chunks.merge()
sizes.calculateSizes(args.bam, chunks)
else:
sizes.calculateSizes(args.bam)
sizes.save(args.out + '.fragmentsizes.txt')
if not args.no_plot:
#make figure
fig = plt.figure()
plt.plot(list(range(sizes.lower, sizes.upper)),
sizes.get(sizes.lower, sizes.upper),
label=args.out)
plt.xlabel("Fragment Size")
plt.ylabel("Frequency")
fig.savefig(args.out + '.fragmentsizes.pdf')
plt.close(fig)
def run_occ(args):
"""run occupancy calling
"""
if args.fasta:
chrs = read_chrom_sizes_from_fasta(args.fasta)
else:
chrs = read_chrom_sizes_from_bam(args.bam)
pwm = PWM.open(args.pwm)
chunks = ChunkList.read(args.bed, chromDict = chrs, min_offset = args.flank + args.upper/2 + max(pwm.up,pwm.down) + args.nuc_sep/2)
chunks.slop(chrs, up = args.nuc_sep/2, down = args.nuc_sep/2)
chunks.merge()
maxQueueSize = args.cores*10
fragment_dist = FragmentMixDistribution(0, upper = args.upper)
if args.sizes is not None:
tmp = FragmentSizes.open(args.sizes)
fragment_dist.fragmentsizes = FragmentSizes(0, args.upper, vals = tmp.get(0,args.upper))
else:
fragment_dist.getFragmentSizes(args.bam, chunks)
fragment_dist.modelNFR()
fragment_dist.plotFits(args.out + '.occ_fit.eps')
fragment_dist.fragmentsizes.save(args.out + '.fragmentsizes.txt')
params = OccupancyParameters(fragment_dist, args.upper, args.fasta, args.pwm, sep = args.nuc_sep, min_occ = args.min_occ,
flank = args.flank, bam = args.bam, ci = args.confidence_interval, step = args.step)
sets = chunks.split(items = args.cores * 5)
pool1 = mp.Pool(processes = max(1,args.cores-1))
out_handle1 = open(args.out + '.occ.bedgraph','w')
out_handle1.close()
out_handle2 = open(args.out + '.occ.lower_bound.bedgraph','w')
out_handle2.close()
out_handle3 = open(args.out + '.occ.upper_bound.bedgraph','w')
out_handle3.close()
write_queue = mp.JoinableQueue(maxsize = maxQueueSize)
write_process = mp.Process(target = _writeOcc, args=(write_queue, args.out))
write_process.start()
peaks_handle = open(args.out + '.occpeaks.bed','w')
peaks_handle.close()
peaks_queue = mp.JoinableQueue()
peaks_process = mp.Process(target = _writePeaks, args=(peaks_queue, args.out))
peaks_process.start()
nuc_dist = np.zeros(args.upper)
for j in sets:
tmp = pool1.map(_occHelper, zip(j,itertools.repeat(params)))
for result in tmp:
nuc_dist += result[0]
write_queue.put(result[1])
peaks_queue.put(result[2])
pool1.close()
pool1.join()
write_queue.put('STOP')
peaks_queue.put('STOP')
write_process.join()
peaks_process.join()
pysam.tabix_compress(args.out + '.occpeaks.bed', args.out + '.occpeaks.bed.gz',force = True)
shell_command('rm ' + args.out + '.occpeaks.bed')
pysam.tabix_index(args.out + '.occpeaks.bed.gz', preset = "bed", force = True)
for i in ('occ','occ.lower_bound','occ.upper_bound'):
pysam.tabix_compress(args.out + '.' + i + '.bedgraph', args.out + '.'+i+'.bedgraph.gz',force = True)
shell_command('rm ' + args.out + '.' + i + '.bedgraph')
pysam.tabix_index(args.out + '.' + i + '.bedgraph.gz', preset = "bed", force = True)
dist_out = FragmentSizes(0, args.upper, vals = nuc_dist)
dist_out.save(args.out + '.nuc_dist.txt')
print "Making figure"
#make figure
fig = plt.figure()
plt.plot(range(0,args.upper),dist_out.get(0,args.upper),label = "Nucleosome Distribution")
plt.xlabel("Fragment Size")
plt.ylabel("Frequency")
fig.savefig(args.out+'.nuc_dist.eps')
plt.close(fig)
