def main():
usage = "\n%prog [options]"
parser = OptionParser(usage,version="%prog " + __version__)
parser.add_option("-i","--input",action="store",dest="input_read",help="Read sequence in fasta or fastq format. Multiple fasta/fastq files should be separated by ','. For example: read.fq,read2.fa,read3,fa ")
parser.add_option("-r","--refgenome",action="store",type="string",dest="ref_genome",help="Reference genome sequence in fasta format. Optional")
parser.add_option("-g","--refgene",action="store",type="string",dest="ref_gene",help="Reference mRNA sequence in fasta format. Optional")
(options,args)=parser.parse_args()
if not options.input_read:
parser.print_help()
sys.exit(0)
read_table={}
read_file_names=[] #base name
read_file_sum = {} #sum of hexamer
for read_file in options.input_read.split(','):
if not file_exist(read_file):
print >>sys.stderr, read_file, ' does NOT exist!'
continue
print >>sys.stderr, "Calculate hexamer of " + read_file + ' file ...',
read_table[os.path.basename(read_file)] = FrameKmer.kmer_freq_file(fastafile = read_file, word_size = 6, step_size = 1, frame = 0)
read_file_names.append(os.path.basename(read_file))
read_file_sum[os.path.basename(read_file)] = float(sum(read_table[os.path.basename(read_file)].values()))
print >>sys.stderr, "Done"
if options.ref_genome and file_exist(options.ref_genome):
print >>sys.stderr, "Calculate hexamer of " + options.ref_genome + ' file ...',
read_table[os.path.basename(options.ref_genome)] = FrameKmer.kmer_freq_file(fastafile = options.ref_genome, word_size = 6, step_size = 1, frame = 0)
read_file_names.append(os.path.basename(options.ref_genome))
read_file_sum[os.path.basename(options.ref_genome)] = float(sum(read_table[os.path.basename(options.ref_genome)].values()))
print >>sys.stderr, "Done."
if options.ref_gene and file_exist(options.ref_gene):
print >>sys.stderr, "Calculate hexamer of " + options.ref_gene + ' file ...',
read_table[os.path.basename(options.ref_gene)]= FrameKmer.kmer_freq_file(fastafile = options.ref_gene, word_size = 6, step_size = 1, frame = 0)
read_file_names.append(os.path.basename(options.ref_gene))
read_file_sum[os.path.basename(options.ref_gene)] = float(sum(read_table[os.path.basename(options.ref_gene)].values()))
print >>sys.stderr, "Done."
print '\n\nHexamer' + '\t' + '\t'.join(read_file_names)
for kmer in FrameKmer.all_possible_kmer(6):
if 'N' in kmer:continue
print kmer + '\t',
try:
print '\t'.join([str(read_table[name][kmer] / (read_file_sum[name])) for name in read_file_names])
except:
print '\t'.join([str(read_table[name][kmer] / (read_file_sum[name]+1)) for name in read_file_names])
def cal_entropy(self,l=3): '''calculate entropy for each sequence''' for (id,seq) in self.seqs.items(): entropy = 0 dna_chars_uniq = FrameKmer.all_possible_kmer(l) dna_len = len(seq) for c in dna_chars_uniq: if 'N' in c: continue prop = seq.count(c)/(1.0*dna_len) if prop ==0: continue information = numpy.log2(1.0/prop) entropy += prop * information yield(id, entropy)
def cal_entropy(self,l=3): '''calculate entropy for each sequence''' for (id,seq) in self.seqs.items(): entropy = 0 dna_chars_uniq = FrameKmer.all_possible_kmer(l) dna_len = len(seq) for c in dna_chars_uniq: if 'N' in c: continue prop = seq.count(c)/(1.0*dna_len) if prop ==0: continue information = numpy.log2(1.0/prop) entropy += prop * information yield(id, entropy)