def main(nb_input, f, directory_name):
# number of input in integer
nb_input=int(nb_input)
# generate the STT using the following function
function=STT_from_output_string(f, nb_input)
# copy of the STT
STT=copy.deepcopy(function)
# check the len of the directory name and complete with zero if lower than 6
while len(directory_name)<6:
directory_name='0'+directory_name
# directory path to store the output files
mypath='../results/'+directory_name
os.makedirs(mypath)
name_output_file=mypath+'/'+directory_name+'_output.txt'
of=open(name_output_file, 'w')
# From the STT, extraction of the caracteristic for the required devices
imp, max_output=extraction_of_constructions(nb_input, function)
strain=0
for construction in imp:
strain+=1
list_integrase=lineage_to_order_inputs(nb_input, construction[0])
title='Strain'+str(strain)
gsm.computational_device(nb_input, list_integrase, construction[1], title, mypath, directory_name)
gsm.legend(nb_input, mypath, directory_name)
if max_output<5:
DNAseq.design_DNAsequence(nb_input, list_integrase, construction[1], str(strain), '', mypath, directory_name)
if nb_input==5:
if f[325]=='1':
strain+=1
gcm.computation_device('50', str(strain), ['1','2','3','4','5'], 'Strain'+str(strain), mypath, directory_name)
if max_output<5:
DNAcomb.design_DNAsequence('50', str(strain), '', mypath, directory_name)
#of.write('For the following sequential program:\n'+str(STT)+'\n\n')
#of.write(str(strain)+' strains are needed.\n\n')
#of.close()
of.write("This "+str(nb_input)+'-input history-dependent function, \n'+str(STT)+', \nis implemented with '+str(strain)+' strain(s).\n\n')
if max_output<5:
of.write('The DNA sequence is generated using <i>E. coli</i> promoters, terminators and GOI sequences.\n')
name_int=['Bxb1', 'Tp901', 'Int5', 'Int7', 'Int3', 'Int4']
name_output=['GFP', 'RFP', 'BFP', 'LacZ']
texte_int=''
texte_int1=''
texte_int2=''
texte_out1=''
texte_out2=''
for name in range(0, nb_input):
if name==nb_input-1:
texte_int1+=(str(name+1))
texte_int2+=(name_int[name]+'.')
else:
texte_int1+=(str(name+1)+', ')
texte_int2+=(name_int[name]+', ')
if nb_input==1:
texte_int=('The integrase '+texte_int1+' corresponds to '+texte_int2)
else:
texte_int=('The integrases '+texte_int1+' correspond respectively to '+texte_int2)
for name in range(0, max_output):
if name==max_output-1:
texte_out1+=(str(name+1))
texte_out2+=(name_output[name]+' ')
else:
texte_out1+=(str(name+1)+', ')
texte_out2+=(name_output[name]+', ')
if nb_input==1:
texte_out=('For the output '+texte_out1+', the '+texte_out2+'gene is used')
else:
texte_out=('For the outputs '+texte_out1+', the '+texte_out2+'genes are used.')
of.write(texte_int+'\n')
of.write(texte_out+'\n\n')
else:
of.write('Generation of DNA sequence file of computational device is not possible using CALIN website as IDs of output gene are biggest than 4. Please refer to <a href="https://github.com/sguiz/calin" target="_blank" class="nav">github</a> for custom DNA generation.\n\n')
of.close()
strain=0
return
def design(output, nb_input, path, directory_name):
# convert the output integer in a binary number
#output=bin(output)[2:]
name_output_file = path + '/' + directory_name + '_output.txt'
of = open(name_output_file, 'w')
# if len of the output does not correspond to the number of input, add 0 to the number
if len(output) < (2**(nb_input)):
for w in range(2**(nb_input) - len(output)):
output = '0' + output
# initialize the on_sate which will be a list of state equal to 1. The states are identifiy by an integer.
on_state = []
off_state = []
# index for input state
x = 0
# screen all output state (all bit), from the lowest bit to the highest one
for c in reversed(output):
# if output is equal to 1
if c == '1':
# add X to the on_state list
on_state.append(x)
else:
off_state.append(x)
x += 1
# obtain the simplification from Cain McKluskey algorithm of the on_state
# pos_imp correspond to a list of string. Number of string correspond to the nb of sub_function
# Each string is composed of X for whatever, 1 for A or 0 for not(A) and the position of the term correspond to the variable.
pos_imp = function_simplification(on_state, off_state)
#print pos_imp
# bioloigcal_implementation is to obtain the explicit biological implement
# inputs are pos_imp (result from QM algo) and the number of inputs
# outputs are the number of inputs, the number of strains needed, the list of computation devices
# and the list of the connection between integrases and variables.
[nb_strain, list_component,
list_int_var] = biological_implementation(pos_imp, nb_input)
of.write("This " + str(nb_input) + '-input Boolean function ' + output +
' is implemented using ' + str(nb_strain) + ' strain(s).\n\n')
of.write(
'DNA sequences are generated using <i>E. coli</i> promoters, terminators and GOI sequences.\n'
)
name_int = ['Bxb1', 'Tp901', 'Int5', 'Int7', 'Int3', 'Int4']
texte_int1 = ''
texte_int2 = ''
for name in range(0, nb_input):
if name == nb_input - 1:
texte_int1 += (str(name + 1))
texte_int2 += (name_int[name] + '.')
else:
texte_int1 += (str(name + 1) + ', ')
texte_int2 += (name_int[name] + ', ')
if nb_input == 1:
texte_int = ('Integrase ' + texte_int1 + ' corresponds to ' +
texte_int2)
else:
texte_int = ('Integrases ' + texte_int1 +
' correspond respectively to ' + texte_int2)
of.write(texte_int + '\n\n')
of.close()
strain = 0
# for each strain, loop in the list of component and list of integrase variable connections
for COMP, X in zip(list_component, list_int_var):
strain += 1
# To represent the computation device with the information of the strain number and of var/int connections
gcm.computation_device(COMP, str(strain), X, 'Strain' + str(strain),
path, directory_name)
# Generation of the DNA sequence
dns.design_DNAsequence(COMP, str(strain), output, path, directory_name)
gcm.legend(nb_input, path, directory_name)