class Genome_2bit: def __init__(self,genome_2bit_file,verbose=False): self.genome=TwoBitFile(open(genome_2bit_file,'rb')) self.chr_len=dict() self.verbose=verbose for chr_id in self.genome.keys(): self.chr_len[chr_id]=len(self.genome[chr_id]) if verbose: print 'Genome initializated' def extract_sequence(self,coordinate,mask_repetitive=False): if mask_repetitive: seq= ''.join([mask(c) for c in self.genome[coordinate.chr_id][coordinate.bpstart-1:coordinate.bpend]]).lower() else: seq= self.genome[coordinate.chr_id][coordinate.bpstart-1:coordinate.bpend].lower() if coordinate.strand=='-': return Sequence.reverse_complement(seq) else: return seq def estimate_background(self): counting={'a':.0,'c':.0,'g':.0,'t':.0} all=0.0 for chr_id in self.genome.keys(): if self.verbose: start_time = time.time() print 'Counting on:',chr_id for nt in counting.keys(): count_nt=self.genome[chr_id][:].lower().count(nt) counting[nt]+=count_nt all+=count_nt print 'elapsed:',time.time() - start_time if self.verbose: print counting for nt in counting.keys(): counting[nt]/=all return counting def write_meme_background(self,filename): counting=self.estimate_background() with open(filename,'w+') as outfile: for nt in counting.keys(): outfile.write('%s\t%2.4f\n' % (nt,counting[nt])) def write_chr_len(self,filename): with open(filename,'w+') as outfile: for chr_id in self.genome.keys(): outfile.write('%s\t%s\n' % (chr_id,self.chr_len[chr_id]) )
class Genome_2bit: def __init__(self,genome_2bit_file,verbose=False): self.genome=TwoBitFile(open(genome_2bit_file,'rb')) self.chr_len=dict() self.verbose=verbose for chr_id in self.genome.keys(): self.chr_len[chr_id]=len(self.genome[chr_id]) if verbose: print 'Genome initializated' def estimate_background(self): counting={'a':.0,'c':.0,'g':.0,'t':.0} all=0.0 for chr_id in self.genome.keys(): if self.verbose: start_time = time.time() print 'Counting on:',chr_id for nt in counting.keys(): count_nt=self.genome[chr_id][:].lower().count(nt) counting[nt]+=count_nt all+=count_nt print 'elapsed:',time.time() - start_time if self.verbose: print counting for nt in counting.keys(): counting[nt]/=all return counting def write_meme_background(self,filename): counting=self.estimate_background() with open(filename,'w+') as outfile: for nt in counting.keys(): outfile.write('%s\t%2.4f\n' % (nt.upper(),counting[nt])) def write_chr_len(self,filename): with open(filename,'w+') as outfile: for chr_id in self.genome.keys(): outfile.write('%s\t%s\n' % (chr_id,self.chr_len[chr_id]) )
class Genome_2bit: def __init__(self, genome_2bit_file, verbose=False): self.genome = TwoBitFile(open(genome_2bit_file, 'rb')) self.chr_len = dict() self.verbose = verbose for chr_id in self.genome.keys(): self.chr_len[chr_id] = len(self.genome[chr_id]) if verbose: print 'Genome initializated' def estimate_background(self): counting = {'a': .0, 'c': .0, 'g': .0, 't': .0} all = 0.0 for chr_id in self.genome.keys(): if self.verbose: start_time = time.time() print 'Counting on:', chr_id for nt in counting.keys(): count_nt = self.genome[chr_id][:].lower().count(nt) counting[nt] += count_nt all += count_nt if self.verbose: print counting for nt in counting.keys(): counting[nt] /= all return counting def write_meme_background(self, filename): counting = self.estimate_background() with open(filename, 'w+') as outfile: for nt in counting.keys(): outfile.write('%s\t%2.4f\n' % (nt.upper(), counting[nt])) def write_chr_len(self, filename): with open(filename, 'w+') as outfile: for chr_id in self.genome.keys(): outfile.write('%s\t%s\n' % (chr_id, self.chr_len[chr_id]))