def test(coef_var, exp, out): exp_file = open(out, "w") expresion_list = map(lambda x: int(x.rsplit()[1]), open(exp, "r")) gene_list = map(lambda x: x.rsplit()[0], open(exp, "r")) n = 0 for i in expresion_list: read_var = round(distrib.valueNormal(coef_var, int(expresion_list[n]))) exp_file.write(str(read_var) + "\n") n += 1
def test(coef_var, exp, out): exp_file = open(out,"w") expresion_list = map(lambda x: int(x.rsplit()[1]), open(exp, "r")) gene_list = map(lambda x: x.rsplit()[0], open(exp, "r")) n = 0 for i in expresion_list: read_var = round(distrib.valueNormal(coef_var, int(expresion_list[n]))) exp_file.write(str(read_var)+"\n") n+=1
def __printReads(gffvar, coef_var): n = 0 # exp_file = open(readsvar+".exp_normal","w") reads_file = open(readsvar + ".fasta", "w") # for i in SeqIO.parse(gffvar + ".utr.fasta", "fasta"): b = open("brucei.gff.utr.fasta", "r") for i in SeqIO.parse(b, "fasta"): read_var = round(distrib.valueNormal(coef_var, int(expresion_list[n]))) reads_list = splicer.generate_reads(i.seq, int(read_var), read_length) # exp_normal en RPKM # exp_normal = (Decimal(str(read_var)) / len(i.seq)) / total_reads # exp_file.write(i.name + "\t" + str(round(exp_normal*10000, 4)) + "\n") j = 0 for read in reads_list: reads_file.write(">" + i.name + "_read_" + str(j) + "\n") reads_file.write(str(read) + "\n") j += 1 n += 1
def __printReads(gffvar, coef_var): n=0 # exp_file = open(readsvar+".exp_normal","w") reads_file = open(readsvar+".fasta","w") # for i in SeqIO.parse(gffvar + ".utr.fasta", "fasta"): b = open("brucei.gff.utr.fasta","r") for i in SeqIO.parse(b, "fasta"): read_var = round(distrib.valueNormal(coef_var, int(expresion_list[n]))) reads_list = splicer.generate_reads(i.seq, int(read_var), read_length) # exp_normal en RPKM # exp_normal = (Decimal(str(read_var)) / len(i.seq)) / total_reads # exp_file.write(i.name + "\t" + str(round(exp_normal*10000, 4)) + "\n") j = 0 for read in reads_list: reads_file.write(">" + i.name + "_read_"+ str(j) + "\n") reads_file.write(str(read) + "\n") j+=1 n+=1