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
