def run(tfea_csv, experiment, outdir, N=500, seed=True):
logfile = ''.join([outdir, '/', experiment, '_LOG.txt'])
sys.stdout = open(logfile, "w")
print(
"Log file for sequences generated based on some back ground distribution. \n"
)
if seed == 0:
np.random.seed()
print("--------------------------------------------------------------")
print("-----------Setting seed for the sequence generator.-----------")
print("Using random seed..............................")
print(
"WARNING: Sequences generated using a random seed can not be reproduced."
)
elif seed is True:
np.random.seed(global_seed())
else:
np.random.seed(seed)
print("--------------------------------------------------------------")
print("-----------Setting seed for the sequence generator.-----------")
print("User defined seed..............................:", seed, "\n")
print("--------------------------------------------------------------")
print("-----------Reading per-base sequence frequency----------------",
"\n")
##get the sequences from teh frequency calculator
position_prob = sequence_input(tfea_csv)
print("--------------------------------------------------------------")
print("-----------Generating sequences-------------------------------",
"\n")
##generate sequences
#sequences_generating = sequence_generator(sequences, experiment, seq_len=seq_len, N = N)
generating_sequences = sequence_generator(bases=['A', 'T', 'G', 'C'],
N=N,
position_feq=position_prob)
generating_headers = fasta_header(experiment, N=N)
print("--------------------------------------------------------------")
print("-----------Writing sequences to fasta file--------------------",
"\n")
##write sequences to fasta file
#write_fasta(sequences_generating, experiment, outdir)
write_fasta(generating_sequences, generating_headers, experiment, outdir)
print("--------------------------------------------------------------")
print("----------------------------DONE------------------------------")
stop_time = int(time.time())
print("Run time :", stop_time - start_time, " seconds")
def gen():
"""Return a fresh new generator object for each test"""
return sequence_generator()