diff --git a/src/primingprob/priming_prob.py b/src/primingprob/priming_prob.py
index 8088b646f85110b8c6136897c4958ba6b9d2044b..fbb93d4a0e33dc654b221784211d388a0db03a13 100644
--- a/src/primingprob/priming_prob.py
+++ b/src/primingprob/priming_prob.py
@@ -1,154 +1,152 @@
-"""Imports."""
+"""Calculates the probability of priming and write the gff file."""
import numpy as np
import scipy.constants # type: ignore
-class Probability:
- """Calculates the probability of priming and write the gff file."""
+def inter_para(input_path):
+ """Open the RIblast output file and read only the parameter lines.
- def inter_para(input_path):
- """Open the RIblast output file and read only the parameter lines.
+ Args:
+ Path to Energies.txt file
- Args:
- Path to Energies.txt file
+ Returns:
+ my_list (list): Contains the paramter lines from Energies.txt
+ """
+ Energies = open(input_path, "r") # ouput of RIblast
- Returns:
- my_list (list): Contains the paramter lines from Energies.txt
- """
- Energies = open(input_path, "r") # ouput of RIblast
+ mylist = [] # all lines of Energies starting with an ID-number
- mylist = [] # all lines of Energies starting with an ID-number
+ for myline in Energies: # Read lines containing needed data
+ if myline[0].isdigit():
+ mylist.append(myline)
+ elif myline[0].isdigit() is False:
+ continue
- for myline in Energies: # Read lines containing needed data
- if myline[0].isdigit():
- mylist.append(myline)
- elif myline[0].isdigit() is False:
- continue
+ Energies.close()
- Energies.close()
+ return(mylist)
- return(mylist)
- def inter_prob(data_list, fasta_path, output_path):
- """Calculate the prob. and write the gff file.
+def inter_prob(data_list, fasta_path, output_path):
+ """Calculate the prob. and write the gff file.
- Args:
- data_list (list): Contains all parameters of Energies.txt
- fasta_path (path): Path to fasta file
- output_path (path): Path to output file
+ Args:
+ data_list (list): Contains all parameters of Energies.txt
+ fasta_path (path): Path to fasta file
+ output_path (path): Path to output file
- Returns:
- gff (file): Gff file contains all the output information
- """
- # count interactions per script through fasta-ID
- fastafile = open(fasta_path, "r")
- id_list = [] # contains list of transcipt IDs
+ Returns:
+ gff (file): Gff file contains all the output information
+ """
+ # count interactions per script through fasta-ID
+ fastafile = open(fasta_path, "r")
+ id_list = [] # contains list of transcipt IDs
- for mylinecounter in fastafile:
- if mylinecounter.startswith(">"):
- a = mylinecounter
- a = mylinecounter.replace(">", "")
- b = a.split()
- c = b[0]
- id_list.append(c)
- elif mylinecounter.startswith(">") is False:
- continue
+ for mylinecounter in fastafile:
+ if mylinecounter.startswith(">"):
+ a = mylinecounter
+ a = mylinecounter.replace(">", "")
+ b = a.split()
+ c = b[0]
+ id_list.append(c)
+ elif mylinecounter.startswith(">") is False:
+ continue
- counter = 0
- counter_list = [] # list of number of interactions per transcript
+ counter = 0
+ counter_list = [] # list of number of interactions per transcript
- for cc in range(0, len(id_list)):
- for dd in range(0, len(data_list)):
- if id_list[cc] in data_list[dd]:
- counter = counter + 1
+ for cc in range(0, len(id_list)):
+ for dd in range(0, len(data_list)):
+ if id_list[cc] in data_list[dd]:
+ counter = counter + 1
- counter_list.append(counter)
- counter = 0
+ counter_list.append(counter)
+ counter = 0
- para_list = []
+ para_list = []
- for i in range(0, len(data_list)):
- x = data_list[i].split(",")
- para_list.append(x)
- # splitting each list item by the "," this results in a 2D list
+ for i in range(0, len(data_list)):
+ x = data_list[i].split(",")
+ para_list.append(x)
+ # splitting each list item by the "," this results in a 2D list
- for j in range(0, len(para_list)):
- del para_list[j][1:-2]
- # only keeps the ID-numer, the interaction
- # energy, and interaction site of both sequences. (still a 2D-list)
+ for j in range(0, len(para_list)):
+ del para_list[j][1:-2]
+ # only keeps the ID-numer, the interaction
+ # energy, and interaction site of both sequences. (still a 2D-list)
- start_end_index = 1 # index of start and end in the list
+ start_end_index = 1 # index of start and end in the list
- for d in range(0, len(para_list)): # Optimize location output
- a = para_list[d][2].split(":")
- a[start_end_index] = a[start_end_index].replace(") ", "")
- a[start_end_index] = a[start_end_index].replace("\n", "")
- a[start_end_index] = a[start_end_index].replace("-", " ")
- a[start_end_index] = a[start_end_index].split(" ")
- para_list[d][2] = a[start_end_index]
+ for d in range(0, len(para_list)): # Optimize location output
+ a = para_list[d][2].split(":")
+ a[start_end_index] = a[start_end_index].replace(") ", "")
+ a[start_end_index] = a[start_end_index].replace("\n", "")
+ a[start_end_index] = a[start_end_index].replace("-", " ")
+ a[start_end_index] = a[start_end_index].split(" ")
+ para_list[d][2] = a[start_end_index]
- for k in range(0, len(para_list)): # type-conversion of ID and E
- for w in range(0, 2): # "2" because first two elements in each sublist are ID and E
- para_list[k][w] = float(para_list[k][w])
+ for k in range(0, len(para_list)): # type-conversion of ID and E
+ for w in range(0, 2): # "2" because first two elements in each sublist are ID and E
+ para_list[k][w] = float(para_list[k][w])
- joule = 4184 # 1kcal = 4184 joule
- inter_energy = 1 # index of inter. energy in list
+ joule = 4184 # 1kcal = 4184 joule
+ inter_energy = 1 # index of inter. energy in list
- for z in range(0, len(para_list)): # from kcal/mol to Joule/mol
- para_list[z][inter_energy] = para_list[z][inter_energy] * joule
+ for z in range(0, len(para_list)): # from kcal/mol to Joule/mol
+ para_list[z][inter_energy] = para_list[z][inter_energy] * joule
- T = 300.15 # Roomtemperature (27 degree celsius) in Kelvin
- KT = scipy.constants.R * T # calculating gas constant R * T
+ T = 300.15 # Roomtemperature (27 degree celsius) in Kelvin
+ KT = scipy.constants.R * T # calculating gas constant R * T
- for u in range(0, len(para_list)): # calculating -E / RT
- para_list[u][inter_energy] = (-(para_list[u][inter_energy])/KT)
+ for u in range(0, len(para_list)): # calculating -E / RT
+ para_list[u][inter_energy] = (-(para_list[u][inter_energy])/KT)
- prob_list = [] # List containing all the prob.
+ prob_list = [] # List containing all the prob.
- for h in range(0, len(para_list)): # calculating the e^(-E/kT)
- probab = np.exp(para_list[h][inter_energy])
- prob_list.append(probab)
- para_list[h][inter_energy] = probab
+ for h in range(0, len(para_list)): # calculating the e^(-E/kT)
+ probab = np.exp(para_list[h][inter_energy])
+ prob_list.append(probab)
+ para_list[h][inter_energy] = probab
- probability_sum = 0 # variable to calculate sum of probabilities per transcipt
- sum_list = [] # List containing all the sums
+ probability_sum = 0 # variable to calculate sum of probabilities per transcipt
+ sum_list = [] # List containing all the sums
- prob_list2 = prob_list.copy()
+ prob_list2 = prob_list.copy()
- for jj in range(0, len(counter_list)):
- for ii in range(0, counter_list[jj]):
- probability_sum = probability_sum + prob_list[ii]
- sum_list.append(probability_sum)
- probability_sum = 0 # setting back to 0, for next interactions
- del prob_list[0:counter_list[jj]]
+ for jj in range(0, len(counter_list)):
+ for ii in range(0, counter_list[jj]):
+ probability_sum = probability_sum + prob_list[ii]
+ sum_list.append(probability_sum)
+ probability_sum = 0 # setting back to 0, for next interactions
+ del prob_list[0:counter_list[jj]]
- real_prob = [] # contains all the normalized probabilities
+ real_prob = [] # contains all the normalized probabilities
- for jj in range(0, len(sum_list)):
- for ii in range(0, counter_list[jj]):
- prob_list2[ii] = prob_list2[ii]/sum_list[jj]
- real_prob.append(prob_list2[ii])
- del prob_list2[0:counter_list[jj]] # Normalized probabilities
+ for jj in range(0, len(sum_list)):
+ for ii in range(0, counter_list[jj]):
+ prob_list2[ii] = prob_list2[ii]/sum_list[jj]
+ real_prob.append(prob_list2[ii])
+ del prob_list2[0:counter_list[jj]] # Normalized probabilities
- for vv in range(0, len(para_list)): # inserting the normalized values in para_list
- para_list[vv][1] = real_prob[vv]
+ for vv in range(0, len(para_list)): # inserting the normalized values in para_list
+ para_list[vv][1] = real_prob[vv]
- final_list = [] # List containing all the final paramters to print
+ final_list = [] # List containing all the final paramters to print
- for bb in range(0, len(sum_list)): # Insert ID in paralist
- for ss in range(0, counter_list[bb]):
- para_list[ss][0] = id_list[bb]
- final_list.append(para_list[ss])
- del para_list[0:counter_list[bb]]
+ for bb in range(0, len(sum_list)): # Insert ID in paralist
+ for ss in range(0, counter_list[bb]):
+ para_list[ss][0] = id_list[bb]
+ final_list.append(para_list[ss])
+ del para_list[0:counter_list[bb]]
- gff = open(output_path, "w+") # gff file
+ gff = open(output_path, "w+") # gff file
- for ll in range(0, len(final_list)): # writing gff file
- gff.write(str(final_list[ll][0]) + # transcript ID
- "\tRIblast\tPriming Site\t" +
- str(final_list[ll][2][1])+"\t" + # start
- str(final_list[ll][2][0])+"\t" + # end
- str(final_list[ll][1])+"\t.\t.\t.\n") # probability
+ for ll in range(0, len(final_list)): # writing gff file
+ gff.write(str(final_list[ll][0]) + # Transcript ID
+ "\tRIblast\tPriming Site\t" +
+ str(final_list[ll][2][1])+"\t" + # Start
+ str(final_list[ll][2][0])+"\t" + # End
+ str(final_list[ll][1])+"\t.\t.\t.\n") # probability
- gff.close
- return final_list
+ gff.close
+ return final_list