def main(study_fasta_file,control_fast_file,out_file, len_mer):
handle = open(out_file,"wb")
record = []
seven_mers = list(product(['A','C','T','G'], repeat = len_mer))
for seven_mer in seven_mers:
seq = "".join(seven_mer)
study_c,study_p = stats(study_fasta_file,">cns",seq)
control_c,control_p = stats(control_fast_file,">cns",seq)
res, enrich = fisher_chi(study_c,study_p,control_c,control_p)
print res
record.append((res,enrich,seven_mer,study_c,study_p,control_c,control_p))
record.sort()
for res,enrich,seven_mer,study_c,study_p,control_c,control_p in record:
w = "{0}\t{1}\t{2}/{3}\t{4}/{5}\t{6}\n".format(seven_mer,enrich,study_c,study_p,control_c,control_p,res)
handle.write(w)
def main(study_fasta_file, control_fast_file, out_file, len_mer):
handle = open(out_file, "wb")
record = []
seven_mers = list(product(['A', 'C', 'T', 'G'], repeat=len_mer))
for seven_mer in seven_mers:
seq = "".join(seven_mer)
study_c, study_p = stats(study_fasta_file, ">cns", seq)
control_c, control_p = stats(control_fast_file, ">cns", seq)
res, enrich = fisher_chi(study_c, study_p, control_c, control_p)
print res
record.append(
(res, enrich, seven_mer, study_c, study_p, control_c, control_p))
record.sort()
for res, enrich, seven_mer, study_c, study_p, control_c, control_p in record:
w = "{0}\t{1}\t{2}/{3}\t{4}/{5}\t{6}\n".format(seven_mer, enrich,
study_c, study_p,
control_c, control_p,
res)
handle.write(w)
def test_stats(self):
# did only ran rices ....
stats('data/rice_v6_setaria64/rice_v6.features.fasta','>')
stats('data/rice_v6_setaria64/rice_v6_setaria64.cns_real.fasta', '>q')
stats('data/rice_t_sorghum_v1/rice_t_sorghum_v1.cns_real.fasta', '>q')
stats('data/rice_t_sorghum_v1/rice_t.features.fasta', '>')
def test_stats(self):
# did only ran rices ....
stats('data/rice_v6_setaria64/rice_v6.features.fasta', '>')
stats('data/rice_v6_setaria64/rice_v6_setaria64.cns_real.fasta', '>q')
stats('data/rice_t_sorghum_v1/rice_t_sorghum_v1.cns_real.fasta', '>q')
stats('data/rice_t_sorghum_v1/rice_t.features.fasta', '>')