def get_nucleotide(args): """Function to obain sequence content around sites""" if not args.out: args.out = '.'.join(os.path.basename(args.bed).split('.')[0:-1]) chunks = ChunkList.read(args.bed, strand_col=args.strand) params = _NucleotideParameters(args.up, args.down, args.fasta, args.dinucleotide) sets = chunks.split(bases=10000) pool = Pool(processes=args.cores) tmp = pool.map(_nucleotideHelper, list(zip(sets, itertools.repeat(params)))) pool.close() pool.join() result = np.zeros(params.matsize) n = 0.0 for i in tmp: result += i[0] n += i[1] result = result // n if args.norm: normfreqs = seq.getNucFreqs(params.fasta, params.nucleotides) result = result / np.reshape(np.repeat(normfreqs, result.shape[1]), result.shape) #save text output out = np.hstack( (np.array(params.nucleotides)[:, np.newaxis], result.astype('|S8'))) np.savetxt(args.out + '.nucfreq.txt', out, delimiter="\t", fmt='%s') #,fmt = '%1.4g')
def get_pwm(args, bases=50000, splitsize=1000): """Functiono obtain PWM around ATAC insertion""" if not args.out: args.out = '.'.join(os.path.basename(args.bam).split('.')[0:-1]) chrs = read_chrom_sizes_from_fasta(args.fasta) if args.bed is None: chunks = ChunkList.convertChromSizes(chrs, splitsize=splitsize, offset=args.flank) sets = chunks.split(items=bases / splitsize) else: chunks = ChunkList.read(args.bed, chromDict=chrs, min_offset=args.flank) sets = chunks.split(bases=bases) params = _PWMParameters(bam=args.bam, up=args.flank, down=args.flank, fasta=args.fasta, lower=args.lower, upper=args.upper, atac=args.atac, sym=args.sym) pool = Pool(processes=args.cores) tmp = pool.map(_pwmHelper, zip(sets, itertools.repeat(params))) pool.close() pool.join() n = 0.0 result = np.zeros((len(params.nucleotides), params.up + params.down + 1)) for i in tmp: result += i[0] n += i[1] result /= n if args.bed: normfreqs = seq.getNucFreqsFromChunkList(chunks, args.fasta, params.nucleotides) else: normfreqs = seq.getNucFreqs(args.fasta, params.nucleotides) result = result / np.reshape(np.repeat(normfreqs, result.shape[1]), result.shape) if args.sym: #Symmetrize left = result[:, 0:(args.flank + 1)] right = result[:, args.flank:] rightflipped = np.fliplr(np.flipud(right)) combined = (left + rightflipped) / 2 result = np.hstack( (combined, np.fliplr(np.flipud(combined[:, 0:args.flank])))) #save pwm = PWM(result, args.flank, args.flank, params.nucleotides) pwm.save(args.out + '.PWM.txt')
def get_pwm(args, bases = 50000, splitsize = 1000): """Functiono obtain PWM around ATAC insertion""" if not args.out: args.out = '.'.join(os.path.basename(args.bam).split('.')[0:-1]) chrs = read_chrom_sizes_from_fasta(args.fasta) if args.bed is None: chunks = ChunkList.convertChromSizes(chrs, splitsize = splitsize, offset = args.flank) sets = chunks.split(items = bases/splitsize) else: chunks = ChunkList.read(args.bed, chromDict = chrs, min_offset = args.flank) sets = chunks.split(bases = bases) params = _PWMParameters(bam = args.bam, up = args.flank, down = args.flank, fasta = args.fasta, lower = args.lower, upper = args.upper, atac = args.atac, sym = args.sym) pool = Pool(processes = args.cores) tmp = pool.map(_pwmHelper, zip(sets,itertools.repeat(params))) pool.close() pool.join() n = 0.0 result = np.zeros((len(params.nucleotides), params.up + params.down + 1)) for i in tmp: result += i[0] n += i[1] result /= n if args.bed: normfreqs = seq.getNucFreqsFromChunkList(chunks, args.fasta, params.nucleotides) else: normfreqs = seq.getNucFreqs(args.fasta, params.nucleotides) result = result / np.reshape(np.repeat(normfreqs,result.shape[1]),result.shape) if args.sym: #Symmetrize left = result[:,0:(args.flank + 1)] right = result[:,args.flank:] rightflipped = np.fliplr(np.flipud(right)) combined = (left + rightflipped) / 2 result = np.hstack((combined, np.fliplr(np.flipud(combined[:,0:args.flank])))) #save pwm = PWM(result, args.flank, args.flank, params.nucleotides) pwm.save(args.out + '.PWM.txt')
def get_nucleotide(args): """Function to obain sequence content around sites""" if not args.out: args.out = '.'.join(os.path.basename(args.bed).split('.')[0:-1]) chunks = ChunkList.read(args.bed, strand_col = args.strand) params = _NucleotideParameters(args.up, args.down, args.fasta, args.dinucleotide) sets = chunks.split(bases = 10000) pool = Pool(processes = args.cores) tmp = pool.map(_nucleotideHelper, zip(sets,itertools.repeat(params))) pool.close() pool.join() result = np.zeros(params.matsize) n = 0.0 for i in tmp: result += i[0] n += i[1] result = result / n if args.norm: normfreqs = seq.getNucFreqs(params.fasta, params.nucleotides) result = result / np.reshape(np.repeat(normfreqs,result.shape[1]),result.shape) #save text output out = np.hstack((np.array(params.nucleotides)[:,np.newaxis], result.astype('|S8'))) np.savetxt(args.out+'.nucfreq.txt', out, delimiter="\t", fmt = '%s')#,fmt = '%1.4g')