def concatenate_all_the_files(sample):
cmds = "cd $sample/accungs_associations; cat *txt>all.txt"
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/cat_txt.cmd"
pbs_jobs.create_pbs_cmd(cmd_file, alias="cat_txt", gmem=3, cmds=cmds, load_python=False)
job_id = pbs_jobs.submit("-v sample='%s' %s" % (sample, cmd_file))
print(job_id)
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Done!")
def blast_muation_creator():
cmds = "for sample in 1 4 5 9 16 17 20; do cd /sternadi/home/volume3/okushnir/AccuNGS/20201008RV-202329127/merged/" \
"patients/Patient_${sample}/20201124_q30_consensusX7/; cat mutations_all.txt | grep -v ref_pos > " \
"mutations_all.txt.cropped ; for file in `ls tmp/*.blast`; do cat $file >> all_parts.blast ; done ; " \
"cat all_parts.blast | cut -f1,2,3 > all_parts.blast.cropped ; done"
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/all_parts.cmd"
pbs_jobs.create_pbs_cmd(cmd_file, alias="all_parts", gmem=3, cmds=cmds, load_python=False)
job_id = pbs_jobs.submit(cmd_file)
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Done!")
def blast_muation_creator(cmds, sample):
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/all_parts.cmd"
pbs_jobs.create_pbs_cmd(cmd_file,
alias="all_parts",
gmem=3,
cmds=cmds,
load_python=False)
job_id = pbs_jobs.submit("-v sample='%s' %s" % (sample, cmd_file))
print("-v sample='%s' %s" % (sample, cmd_file))
print(job_id)
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Done!")
def main(args):
# def main():
sample = args.sample
# patient_no = str(sample).split("/")[-3].split("_")[-1]
"""1. Create all_parts.blast, all_parts.blast.cropped, mutations_all.txt.cropped"""
# cmds = "for sample in 1 4 5 9 16 17 20; do cd /sternadi/home/volume3/okushnir/AccuNGS/20201008RV-202329127/merged/patients/Patient_$sample/20201017_q30_consensusX5/; cat mutations_all.txt | grep -v ref_pos > mutations_all.txt.cropped ; for file in `ls tmp/*.blast`; do cat $file >> all_parts.blast ; done ; cat all_parts.blast | cut -f1,2,3 > all_parts.blast.cropped ; done"
# cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/all_parts.cmd"
# pbs_jobs.create_pbs_cmd(cmd_file, alias="all_parts", gmem=3, cmds=cmds, load_python=False)
# job_id = pbs_jobs.submit(cmd_file)
# status = pbs_jobs.check_pbs(job_id)
# if status == "Done":
# print("Done!")
"""2. Run variants_on_same_read.py"""
cmds = "base=$sample\n" \
"freqs=`ls ${base} | grep .freqs`\n" \
"echo ${freqs}\n" \
"mkdir ${base}/accungs_associations\n" \
"python /sternadi/home/volume3/okushnir/PhD/variants_on_same_read.py ${base}/all_parts.blast.cropped ${base}/mutations_all.txt.cropped $PBS_ARRAY_INDEX ${base}/${freqs} > ${base}/accungs_associations/$PBS_ARRAY_INDEX.txt"
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/co_occur.cmd"
section_lst = ["2000-3335"] # "336-1999",
for jnum in section_lst:
cmds = "base=$sample\n" \
"freqs=`ls ${base} | grep freqs`\n" \
"mkdir ${base}/accungs_associations\n" \
"python /sternadi/home/volume3/okushnir/PhD/variants_on_same_read.py ${base}/all_parts.blast.cropped ${base}/mutations_all.txt.cropped $PBS_ARRAY_INDEX ${base}/${freqs} > ${base}/accungs_associations/$PBS_ARRAY_INDEX.txt"
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/co_occur.cmd"
pbs_jobs.create_array_pbs_cmd(cmd_file,
jnum,
alias="accungs_assoc",
gmem=3,
cmds=cmds)
print("qsub -v sample='%s' %s" % (sample, cmd_file))
job_id = pbs_jobs.submit("-v sample='%s' %s" % (sample, cmd_file))
# print(job_id)
job_id = job_id.replace("[]", "")
print(job_id)
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Done %s" % (jnum))
print("Done!!!!")
"""3. Concatenate all the files"""
# cmds = "cd $sample/accungs_associations; cat *txt>all.txt"
# cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/cat_txt.cmd"
# pbs_jobs.create_pbs_cmd(cmd_file, alias="cat_txt", gmem=3, cmds=cmds, load_python=False)
# job_id = pbs_jobs.submit("-v sample='%s' %s" % (sample, cmd_file))
# print(job_id)
# status = pbs_jobs.check_pbs(job_id)
# if status == "Done":
# print("Done!")
"""4. Run collect_cooccurs and merge it to freqs file"""
def running_variants_on_the_same_read(sample, section_lst):
for jnum in section_lst:
cmds = "base=$sample\n" \
"freqs=`ls ${base} | grep freqs`\n" \
"mkdir ${base}/accungs_associations\n" \
"python /sternadi/home/volume1/maozgelbart/variants_on_same_read.py ${base}/all_parts.blast.cropped ${base}/mutations_all.txt.cropped $PBS_ARRAY_INDEX ${base}/${freqs} > ${base}/accungs_associations/$PBS_ARRAY_INDEX.txt"
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/co_occur.cmd"
pbs_jobs.create_array_pbs_cmd(cmd_file, jnum, alias="accungs_assoc", gmem=3, cmds=cmds)
print("qsub -v sample='%s' %s" % (sample, cmd_file))
job_id = pbs_jobs.submit("-v sample='%s' %s" % (sample, cmd_file))
# print(job_id)
job_id = job_id.replace("[]", "")
print(job_id)
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Done %s" % (jnum))
print("Done!!!!")
def main(args):
virus = args.virus
passages = args.passages
without_passage = args.without
from_passage = int(passages.split("p")[1].split("-")[0])
to_passage = int(passages.split("-p")[1])
no_generations = to_passage
input_dir = args.input_dir # directory contains q23_data_mutation.csv - "/Volumes/STERNADILABHOME$/volume3/okushnir/Cirseq/PV/OPV/39mixMOI/"
pipline_quality = args.quality
mutation_type = args.mutation_type
replica_no = args.replica_no
mutation_all_at_once = args.mutation_all_at_once
fits_dir = input_dir + "fits/"
try:
os.mkdir(fits_dir)
except OSError:
print("Creation of the directory %s failed" % fits_dir)
else:
print("Successfully created the directory %s " % fits_dir)
fits_input_dir = fits_dir + "input/"
try:
os.mkdir(fits_input_dir)
except OSError:
print("Creation of the directory %s failed" % fits_input_dir)
else:
print("Successfully created the directory %s " % fits_input_dir)
fits_input_pass_dir = fits_input_dir + "%s/" % passages
try:
os.mkdir(fits_input_pass_dir)
except OSError:
print("Creation of the directory %s failed" % fits_input_pass_dir)
else:
print("Successfully created the directory %s " % fits_input_pass_dir)
mutation_lst = ["CU", "AG", "AG_adar", "AG_nonadar", "GA", "UC"]
fits_input_dir = input_dir + "fits/input/%s/" % passages
"""1. Create fits dataset from data_mutation.csv file"""
print("Creating fits dataset from data_mutation.csv file...")
start_pos_dict = {"OPV": 3832, "RVB14": 3635, "CVB3": 3745, "PV": 3833} # start from 2B for all viruses
start_position = checkKey(start_pos_dict, virus)
fits_data_construction(input_dir, fits_input_pass_dir, from_passage, to_passage, pipline_quality, start_position,
replica_no, without_passage)
# break the dataset to positions datasets
print("breaking the dataset to positions sub-datasets")
for mutation in mutation_lst:
df_mutation = pd.read_csv(fits_input_pass_dir + "final_%sMutations_sorted_%s.txt" % (mutation_type, mutation), sep="\t")
fits_input_pass_mutation_dir = fits_input_pass_dir + "%s" % mutation
try:
os.mkdir(fits_input_pass_mutation_dir)
except OSError:
print("Creation of the directory %s failed" % fits_input_pass_mutation_dir)
else:
print("Successfully created the directory %s " % fits_input_pass_mutation_dir)
for position in df_mutation["pos"].iloc[0:-1]:
df_pos = df_mutation.groupby(["pos"]).get_group(position)
df_pos.to_csv(fits_input_pass_dir + "%s/final_%sMutations_sorted_%s.txt" % (mutation, mutation_type, position), index=False,
sep="\t")
"""2. Run FITS_jobarray_mutation.cmd"""
if virus == "OPV":
no_generations = (to_passage*2)+1
else:
no_generations = to_passage
with open(fits_input_dir+"parameters_mutation.txt", "w") as parameter_mutation:
parameter_mutation.write("# basic parameters\n"
"N 1000000\n"
"num_alleles 2\n"
"num_generations %s\n"
"min_log_mutation_rate0_0 -9\n"
"min_log_mutation_rate0_1 -9\n"
"min_log_mutation_rate1_0 -9\n"
"min_log_mutation_rate1_1 -9\n"
"max_log_mutation_rate0_0 -3\n"
"max_log_mutation_rate0_1 -3\n"
"max_log_mutation_rate1_0 -3\n"
"max_log_mutation_rate1_1 -3\n"
"# bottleneck\n"
"bottleneck_interval 2\n"
"bottleneck_size 1000000\n"
"fitness_allele0 1.0\n"
"fitness_allele1 1.0\n"
"num_samples_from_prior 100000\n"
"acceptance_rate 0.01" % (no_generations))
try:
os.mkdir(input_dir + "fits/output/")
except OSError:
print("Creation of the directory %s failed" % input_dir + "fits/output/")
else:
print("Successfully created the directory %s " % input_dir + "fits/output/")
try:
os.mkdir(input_dir + "fits/output/mutation/")
except OSError:
print("Creation of the directory %s failed" % input_dir + "fits/output/mutation/")
else:
print("Successfully created the directory %s " % input_dir + "fits/output/mutation/")
fits_mutation_output_dir = input_dir + "fits/output/mutation/%s/" % passages
try:
os.mkdir(fits_mutation_output_dir)
except OSError:
print("Creation of the directory %s failed" % fits_mutation_output_dir)
else:
print("Successfully created the directory %s " % fits_mutation_output_dir)
if mutation_all_at_once == "off":
if mutation_type == "all":
cmds = "module load gcc/gcc-8.2.0\n" \
"VIRUS=$VIRUS\n" \
"PASSAGES=$PASSAGES\n" \
"fits_dir=$fits_dir\n" \
"PARAM='mutation'\n" \
"namesj=('AG' 'UC' 'GA' 'CU' 'AG_adar' 'AG_nonadar')\n"\
"j=$(($[PBS_ARRAY_INDEX-1]%${#namesj[@]}))\n"\
"i=$(($[PBS_ARRAY_INDEX-1-j]/${#namesj[@]}))\n" \
"element=$(ls ${fits_dir}/input/${PASSAGES}/${namesj[j]}| grep 'all'| grep -oh '[0-9]'*)\n"\
"namesi=($element)\n" \
"for element in '${namesi[@]}';do echo '$element';done\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}\n" \
"/sternadi/home/volume1/talzinger/FITS_Analyses/FITS_bin/fits1.3.3 -$PARAM ${fits_dir}/input/${PASSAGES}/" \
"parameters_${PARAM}.txt ${fits_dir}/input/${PASSAGES}/${namesj[j]}/final_allMutations_sorted_" \
"${namesi[i]}.txt ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/posterior_${PARAM}_all_${namesi[i]}.txt " \
"${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/summary_${PARAM}_all_${namesi[i]}.txt"
if mutation_type == "syn":
cmds = "module load gcc/gcc-8.2.0\n" \
"VIRUS=$VIRUS\n" \
"PASSAGES=$PASSAGES\n" \
"fits_dir=$fits_dir\n" \
"PARAM='mutation'\n" \
"namesj=('AG' 'UC' 'GA' 'CU' 'AG_adar' 'AG_nonadar')\n"\
"j=$(($[PBS_ARRAY_INDEX-1]%${#namesj[@]}))\n"\
"i=$(($[PBS_ARRAY_INDEX-1-j]/${#namesj[@]}))\n" \
"element=$(ls ${fits_dir}/input/${PASSAGES}/${namesj[j]}| grep 'syn'| grep -oh '[0-9]'*)\n"\
"namesi=($element)\n" \
"for element in '${namesi[@]}';do echo '$element';done\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}\n" \
"/sternadi/home/volume1/talzinger/FITS_Analyses/FITS_bin/fits1.3.3 -$PARAM ${fits_dir}/input/${PASSAGES}/" \
"parameters_${PARAM}.txt ${fits_dir}/input/${PASSAGES}/${namesj[j]}/final_synMutations_sorted_" \
"${namesi[i]}.txt ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/posterior_${PARAM}_syn_${namesi[i]}.txt " \
"${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/summary_${PARAM}_syn_${namesi[i]}.txt"
part_lst = []
for mutation in mutation_lst:
list = os.listdir(fits_input_dir + mutation) # dir is your directory path
number_files = len(list)
part_lst.append(number_files)
n = max(part_lst)
print(n)
a1 = 1
d = len(mutation_lst)
jnum_tmp = a1 + d * (n - 1)
print(jnum_tmp)
jnum_quarter = int(np.round(jnum_tmp/4))
jnum1 = "1-%s" % (str(jnum_quarter))
jnum2 = "%s-%s" % (str(jnum_quarter+1), str(2*jnum_quarter))
jnum3 = "%s-%s" % (str((2*jnum_quarter)+1), str(3*jnum_quarter))
jnum4 = "%s-%s" % (str((3*jnum_quarter)+1), str(4*jnum_quarter))
jnum_lst = [jnum1, jnum2, jnum3, jnum4]
for jnum in jnum_lst:
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/new_FITS_jobarray_mutation_%s.cmd" % virus
pbs_jobs.create_array_pbs_cmd(cmd_file, jnum, alias="Fits_mutation", gmem=3, cmds=cmds)
print("qsub -v VIRUS='%s',PASSAGES='%s', fits_dir='%s' %s" % (virus, passages, fits_dir, cmd_file))
job_id = pbs_jobs.submit("-v VIRUS='%s',PASSAGES='%s, fits_dir=%s' %s" % (virus, passages, fits_dir, cmd_file))
job_id = job_id.split("[")[0]
print("Running new_FITS_jobarray_mutation_%s.cmd, job_id:%s" % (virus, job_id))
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Done: %s" % jnum)
# For all position at once
else:
cmds_all = "module load gcc/gcc-8.2.0\n" \
"VIRUS=$VIRUS\n" \
"PASSAGES=$PASSAGES\n" \
"fits_dir=$fits_dir\n" \
"PARAM='mutation'\n" \
"namesj=('AG' 'UC' 'GA' 'CU' 'AG_adar' 'AG_nonadar')\n" \
"namesi=('syn')\n" \
"j=$(($[PBS_ARRAY_INDEX-1]%${#namesj[@]}))\n" \
"i=$(($[PBS_ARRAY_INDEX-1-j]/${#namesj[@]}))\n"\
"/sternadi/home/volume1/talzinger/FITS_Analyses/FITS_bin/fits1.3.3 -$PARAM " \
"${fits_dir}/input/${PASSAGES}/parameters_$" \
"{PARAM}.txt ${fits_dir}/input/${PASSAGES}/" \
"final_${namesi[i]}Mutations_sorted_${namesj[j]}.txt ${fits_dir}/output/${PARAM}/${PASSAGES}/" \
"posterior_${PARAM}_${namesi[$i]}_${namesj[$j]}.txt " \
"${fits_dir}/output/${PARAM}/${PASSAGES}/summary_${PARAM}_${namesi[$i]}_${namesj[$j]}.txt"
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/FITS_mutation_%s.cmd" % virus
jnum_all = "1-6"
pbs_jobs.create_array_pbs_cmd(cmd_file, jnum_all, alias="Fits_mutation", gmem=3, cmds=cmds_all)
print("qsub -v VIRUS='%s',PASSAGES='%s, fits_dir=%s' %s" % (virus, passages, fits_dir, cmd_file))
job_id = pbs_jobs.submit("-v VIRUS='%s',PASSAGES='%s, fits_dir=%s' %s" % (virus, passages, fits_dir, cmd_file))
job_id = job_id.split("[")[0]
print("Running FITS_mutation_%s.cmd, job_id:%s" % (virus, job_id))
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Mutation rate AllAtOnce is DONE!")
"""3. Run fits_mutation_united"""
if mutation_all_at_once == "off":
if mutation_type == "all":
for mutation in mutation_lst:
output_mutation_dir = input_dir + "fits/output/mutation/%s/%s/" % (passages, mutation)
output_file = output_mutation_dir + "all.txt"
print("Creating the mutation conjugated report of: %s" % output_mutation_dir)
fits_mutation_united_all.fits_mutation_united_all(output_mutation_dir, output_file)
if mutation_type == "syn":
for mutation in mutation_lst:
output_mutation_dir = input_dir + "fits/output/mutation/%s/%s/" % (passages, mutation)
output_file = output_mutation_dir + "all.txt"
print("Creating the mutation conjugated report of: %s" % output_mutation_dir)
fits_mutation_united_syn.fits_mutation_united_syn(output_mutation_dir, output_file)
"""4. Run fits_parameters.py"""
print("Creating fitness parameters")
fits_parameters_pos.fitness_parameters_pos(input_dir=fits_mutation_output_dir, output_dir=fits_input_dir)
"""5. Run new_FITS_jobarray_fitness.cmd"""
try:
os.mkdir(input_dir + "fits/output/fitness/")
except OSError:
print("Creation of the directory %s failed" % (input_dir + "fits/output/fitness/"))
else:
print("Successfully created the directory %s " % (input_dir + "fits/output/fitness/"))
if mutation_type == "all":
cmds = "module load gcc/gcc-8.2.0\n" \
"VIRUS=$VIRUS\n" \
"PASSAGES=$PASSAGES\n" \
"fits_dir=$fits_dir\n" \
"PARAM='fitness'\n" \
"namesj=('AG' 'UC' 'GA' 'CU' 'AG_adar' 'AG_nonadar')\n"\
"j=$(($[PBS_ARRAY_INDEX-1]%${#namesj[@]}))\n"\
"i=$(($[PBS_ARRAY_INDEX-1-j]/${#namesj[@]}))\n" \
"element=$(ls ${fits_dir}/input/${PASSAGES}/${namesj[j]}| grep 'all'| grep -oh '[0-9]'*)\n"\
"namesi=($element)\n" \
"for element in '${namesi[@]}';do echo '$element';done\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}\n" \
"/sternadi/home/volume1/talzinger/FITS_Analyses/FITS_bin/fits1.3.3 -$PARAM ${fits_dir}/input/${PASSAGES}/" \
"parameters_${PARAM}_${namesj[j]}.txt ${fits_dir}/input/${PASSAGES}/${namesj[j]}/final_allMutations_sorted_" \
"${namesi[i]}.txt ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/posterior_${PARAM}_all_${namesi[i]}.txt " \
"${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/summary_${PARAM}_all_${namesi[i]}.txt"
if mutation_type == "syn":
cmds = "module load gcc/gcc-8.2.0\n" \
"VIRUS=$VIRUS\n" \
"PASSAGES=$PASSAGES\n" \
"fits_dir=$fits_dir\n" \
"PARAM='fitness'\n" \
"namesj=('AG' 'UC' 'GA' 'CU' 'AG_adar' 'AG_nonadar')\n"\
"j=$(($[PBS_ARRAY_INDEX-1]%${#namesj[@]}))\n"\
"i=$(($[PBS_ARRAY_INDEX-1-j]/${#namesj[@]}))\n" \
"element=$(ls ${fits_dir}/input/${PASSAGES}/${namesj[j]}| grep 'syn'| grep -oh '[0-9]'*)\n"\
"namesi=($element)\n" \
"for element in '${namesi[@]}';do echo '$element';done\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}\n" \
"mkdir ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}\n" \
"/sternadi/home/volume1/talzinger/FITS_Analyses/FITS_bin/fits1.3.3 -$PARAM ${fits_dir}/input/${PASSAGES}/" \
"parameters_${PARAM}_${namesj[j]}.txt ${fits_dir}/input/${PASSAGES}/${namesj[j]}/final_synMutations_sorted_" \
"${namesi[i]}.txt ${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/posterior_${PARAM}_syn_${namesi[i]}.txt " \
"${fits_dir}/output/${PARAM}/${PASSAGES}/${namesj[j]}/summary_${PARAM}_syn_${namesi[i]}.txt"
part_lst = []
for mutation in mutation_lst:
list = os.listdir(fits_input_dir + mutation) # dir is your directory path
number_files = len(list)
part_lst.append(number_files)
n = max(part_lst)
print(n)
a1 = 1
d = len(mutation_lst)
jnum_tmp = a1 + d * (n - 1)
print(jnum_tmp)
jnum_quarter = int(np.round(jnum_tmp/4))
jnum1 = "1-%s" % (str(jnum_quarter))
jnum2 = "%s-%s" % (str(jnum_quarter+1), str(2*jnum_quarter))
jnum3 = "%s-%s" % (str((2*jnum_quarter)+1), str(3*jnum_quarter))
jnum4 = "%s-%s" % (str((3*jnum_quarter)+1), str(4*jnum_quarter))
jnum_lst = [jnum1, jnum2, jnum3, jnum4]
for jnum in jnum_lst:
cmd_file = "/sternadi/home/volume3/okushnir/Cluster_Scripts/new_FITS_jobarray_fitness_%s.cmd" % virus
pbs_jobs.create_array_pbs_cmd(cmd_file, jnum, alias="Fits_fitness", gmem=3, cmds=cmds)
print("qsub -v VIRUS='%s',PASSAGES='%s', fits_dir='%s' %s" % (virus, passages, fits_dir, cmd_file))
job_id = pbs_jobs.submit("-v VIRUS='%s',PASSAGES='%s, fits_dir=%s' %s" % (virus, passages, fits_dir, cmd_file))
job_id = job_id.split("[")[0]
print("Running new_FITS_jobarray_fitness_%s.cmd, job_id:%s" % (virus, job_id))
status = pbs_jobs.check_pbs(job_id)
if status == "Done":
print("Done: %s" % jnum)
"""6. Run fits_fitness_united"""
if mutation_type == "all":
for mutation in mutation_lst:
output_fitness_dir = input_dir + "fits/output/fitness/%s/%s/" % (passages, mutation)
output_file = output_fitness_dir + "all.txt"
print("Creating the fitness conjugated report of: %s" % output_fitness_dir)
fits_fitness_united_all(output_fitness_dir, output_file)
if mutation_type == "syn":
for mutation in mutation_lst:
output_fitness_dir = input_dir + "fits/output/fitness/%s/%s/" % (passages, mutation)
output_file = output_fitness_dir + "all.txt"
print("Creating the fitness conjugated report of: %s" % output_fitness_dir)
fits_fitness_united_syn(output_fitness_dir, output_file)