diff --git a/src/PrimingProb.py b/src/PrimingProb.py
deleted file mode 100644
index bb755fc731b4746c76517a34a544e5f566daeaf6..0000000000000000000000000000000000000000
--- a/src/PrimingProb.py
+++ /dev/null
@@ -1,101 +0,0 @@
-"""Imports."""
-import numpy as np
-import scipy.constants
-
-
-class Probability:
- """Calculates the probability of priming and write the gff file."""
-
- def InterPara():
- """Open the RIblast output file and read only the parameter lines.
-
- Args:
- None
-
- Returns:
- my_list (list): Contains all the paramter lines from RIblast
- """
- myfile = open("./Docker-Files/Energies.txt", "r") # ouput of RIblast
-
- mylist = [] # all lines of Energies starting with an ID-number
-
- for myline in myfile: # Read lines containing needed data
- if myline[0].isdigit():
- mylist.append(myline)
- else:
- continue
- myfile.close()
-
- return(mylist)
-
- data = InterPara()
-
- def InterProb(data_list):
- """Calculate the prob. and make the gff file.
-
- Args:
- data_list (list): Contains all parameters of RIblast
-
- Returns:
- gff (file): Gff file contains all the output information
- """
- 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 2-D 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 d in range(0, len(para_list)): # Optimize location output
- a = para_list[d][2].split(":")
- a[1] = a[1].replace(") ", "")
- a[1] = a[1].replace("\n", "")
- a[1] = a[1].replace("-", " ")
- a[1] = a[1].split(" ")
- para_list[d][2] = a[1]
-
- for k in range(0, len(para_list)): # type-conversion of ID and E
- for l in range(0, 2):
- para_list[k][l] = float(para_list[k][l])
-
- for z in range(0, len(para_list)): # from kcal/mol to Joule/mol
- para_list[z][1] = para_list[z][1] * 4184
-
- kT = scipy.constants.R * 300.15 # calculating gas constant R * T
-
- for u in range(0, len(para_list)): # calculating -E / RT
- para_list[u][1] = (-(para_list[u][1])/kT)
-
- 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][1])
- prob_list.append(probab)
- para_list[h][1] = probab
-
- prob_list_sum = sum(prob_list) # Sum of all probabilities
- real_prob = []
-
- for v in range(0, len(para_list)): # Normalized probabilities
- prob_linear = (para_list[v][1])/prob_list_sum
- real_prob.append(prob_linear)
- para_list[v][1] = prob_linear
-
- gff = open("./output/Potential_Priming_sites.txt", "w+") # gff file
-
- for i in range(0, len(para_list)):
- gff.write("Interactions: "+str(para_list[i][0]) +
- "\tRIblast\ttranscript\t"+str(para_list[i][2][1])+"\t" +
- str(para_list[i][2][0])+"\t" +
- str(para_list[i][1])+"\t.\t.\t.\n")
-
- gff.close
-
- return gff
-
- InterProb(data)
diff --git a/src/PrimingProb_Final.py b/src/PrimingProb_Final.py
new file mode 100644
index 0000000000000000000000000000000000000000..a1adb8cd7d41561c29812cae8c13addb21805052
--- /dev/null
+++ b/src/PrimingProb_Final.py
@@ -0,0 +1,173 @@
+"""Imports."""
+import numpy as np
+import scipy.constants
+import argparse
+from pathlib import Path
+
+
+class Probability:
+ """Calculates the probability of priming and write the gff file."""
+
+ # adding parser
+ parser = argparse.ArgumentParser(
+ description="Fasta-file input",
+ add_help=False,
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
+ # add arguments
+ parser.add_argument(
+ 'input_file',
+ type=lambda p: Path(p).absolute(),
+ metavar="PATH",
+ help="path to fasta-file",
+ )
+
+ args = parser.parse_args()
+
+ def InterPara(path):
+ """Open the RIblast output file and read only the parameter lines.
+
+ Args:
+ Path to Fasta-file
+
+ Returns:
+ my_list (list): Contains all the paramter lines from RIblast
+ """
+ # myfile = open(sys.argv[1], "r") # ouput of RIblast
+ myfile = open(path, "r")
+
+ mylist = [] # all lines of Energies starting with an ID-number
+
+ for myline in myfile: # Read lines containing needed data
+ if myline[0].isdigit():
+ mylist.append(myline)
+ else:
+ continue
+
+ myfile.close()
+
+ return(mylist)
+
+ data = InterPara(args.input_file)
+
+ def InterProb(data_list):
+ """Calculate the prob. and make the gff file.
+
+ Args:
+ data_list (list): Contains all parameters of RIblast
+
+ Returns:
+ gff (file): Gff file contains all the output information
+ """
+ # count interactions per script through fasta ID (first line of fasta)
+ mycounter = open("./Docker-Files/transcript.fasta", "r")
+
+ mycounter_list = []
+
+ for mylinecounter in mycounter:
+ if mylinecounter.startswith(">"):
+ a = mylinecounter
+ a = mylinecounter.replace(">", "")
+ b = a.replace("\n", "")
+ mycounter_list.append(b)
+ else:
+ continue
+
+ counter = 0
+ counter_list = []
+
+ for cc in range(0, len(mycounter_list)):
+ for dd in range(0, len(data_list)):
+ if mycounter_list[cc] in data_list[dd]:
+ counter = counter + 1
+ else:
+ continue
+ counter_list.append(counter)
+ counter = 0
+
+ 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 2-D 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 d in range(0, len(para_list)): # Optimize location output
+ a = para_list[d][2].split(":")
+ a[1] = a[1].replace(") ", "")
+ a[1] = a[1].replace("\n", "")
+ a[1] = a[1].replace("-", " ")
+ a[1] = a[1].split(" ")
+ para_list[d][2] = a[1]
+
+ for k in range(0, len(para_list)): # type-conversion of ID and E
+ for w in range(0, 2):
+ para_list[k][w] = float(para_list[k][w])
+
+ for z in range(0, len(para_list)): # from kcal/mol to Joule/mol
+ para_list[z][1] = para_list[z][1] * 4184
+
+ kT = scipy.constants.R * 300.15 # calculating gas constant R * T
+
+ for u in range(0, len(para_list)): # calculating -E / RT
+ para_list[u][1] = (-(para_list[u][1])/kT)
+
+ 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][1])
+ prob_list.append(probab)
+ para_list[h][1] = probab
+
+ count_sum = 0
+ sum_list = []
+
+ prob_list2 = prob_list.copy()
+
+ for jj in range(0, len(counter_list)):
+ for ii in range(0, counter_list[jj]):
+ count_sum = count_sum + prob_list[ii]
+ sum_list.append(count_sum)
+ count_sum = 0
+ del prob_list[0:counter_list[jj]]
+
+ real_prob = []
+
+ 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
+
+ # real_prob contains all the linearized probabilities
+
+ for vv in range(0, len(para_list)):
+ para_list[vv][1] = real_prob[vv]
+
+ final_list = []
+
+ for bb in range(0, len(sum_list)): # Insert ID in paralist
+ for ss in range(0, counter_list[bb]):
+ para_list[ss][0] = mycounter_list[bb]
+ final_list.append(para_list[ss])
+ del para_list[0:counter_list[bb]]
+
+ gff = open("./output/Potential_Priming_sites.txt", "w+") # gff file
+
+ for ll in range(0, len(final_list)):
+ gff.write(str(final_list[ll][0]) +
+ "\tRIblast\ttranscript\t" +
+ str(final_list[ll][2][1])+"\t" +
+ str(final_list[ll][2][0])+"\t" +
+ str(final_list[ll][1])+"\t.\t.\t.\n")
+
+ gff.close
+
+ return gff
+
+ InterProb(data)
diff --git a/src/RIblast_process2.nf b/src/RIblast_process3.nf
similarity index 93%
rename from src/RIblast_process2.nf
rename to src/RIblast_process3.nf
index 66f1017b11f5adc3bb946cbcdb3aa1b5d5bfb35b..eb35b4cdb1fdf4d208af6f5fa8dc694bb532c274 100644
--- a/src/RIblast_process2.nf
+++ b/src/RIblast_process3.nf
@@ -1,6 +1,6 @@
#!/usr/bin/env nextflow
-params.transcripts = "$baseDir/Docker-Files/transcript3.fasta"
+params.transcripts = "$baseDir/Docker-Files/transcript2.fasta"
params.primers = "$baseDir/Docker-Files/primer.fasta"
log.info """\
@@ -23,3 +23,4 @@ process RIblast_interaction {
RIblast ris -i $primer -o /RIblast/Energies.txt -d /RIblast/test_db
"""
}
+
diff --git a/src/parameter_parser.py b/src/parameter_parser.py
new file mode 100644
index 0000000000000000000000000000000000000000..61af08e707a9cf3485432b50007ea516dc8f15ae
--- /dev/null
+++ b/src/parameter_parser.py
@@ -0,0 +1,72 @@
+"""Module containing functionalities to store run parameters.
+
+Class:
+ ParamParse: Take as input a file containing the parameters
+ and stores them in its attributes.
+"""
+import logging
+from pathlib import Path
+
+LOG = logging.getLogger(__name__)
+
+
+class ParamParse:
+ """Class holding the parameters of the run.
+
+ Args:
+ param_file: Path to file with parameter values.
+
+ Attributes:
+ param_file: File with parameter values.
+ transcripts_file: File with transcript abundances.
+ genome_ref_file: Reference genome file.
+ annotations_file: Transcripts annotations.
+ output_path: Output folder.
+ n_reads: Number of reads to be simulated.
+ n_cells: Number of cells to be simulated.
+ rna_avg_length: average RNA fragment length.
+ rna_sd_length: RNA fragment length standard deviation.
+ read_length: Read length.
+ intron_rate: Constant probability of retaining an intron.
+ add_poly_a: Boolean option to add a poly A tail.
+ poly_a_func: Function to add a poly_a tail.
+ primer_seq: Sequence of the primer.
+ priming_func: Function that evaluates internal priming.
+ """
+
+ def __init__(self, param_file: Path) -> None:
+ """Class constructor."""
+ self.param_file: Path = Path(param_file)
+ with open(param_file) as f:
+ LOG.info("Loading parameters...")
+ for line in f:
+ s = line.split(':')
+ if s[0] == 'Csv transcripts file':
+ self.transcripts_file: Path = Path(s[1].strip())
+ elif s[0] == 'Reference genome file':
+ self.genome_ref_file: Path = Path(s[1].strip())
+ elif s[0] == 'Transcripts annotation file':
+ self.annotations_file: Path = Path(s[1].strip())
+ elif s[0] == 'Output folder':
+ self.output_path: Path = Path(s[1].strip())
+ elif s[0] == 'Number of reads':
+ self.n_reads: int = int(s[1].strip())
+ elif s[0] == 'Number of cells':
+ self.n_cells: int = int(s[1].strip())
+ elif s[0] == 'Average RNA fragments length':
+ self.rna_avg: float = float(s[1].strip())
+ elif s[0] == 'RNA fragment length standard deviation':
+ self.rna_sd_length: float = float(s[1].strip())
+ elif s[0] == 'Reads length':
+ self.read_length: int = int(s[1].strip())
+ elif s[0] == 'Intron retaining probability':
+ self.intron_rate: float = float(s[1].strip())
+ elif s[0] == 'Add poly A tail':
+ self.add_poly_a: bool = bool(s[1].strip())
+ elif s[0] == 'Function to add poly A tail':
+ self.poly_a_func: str = str(s[1].strip())
+ elif s[0] == 'Primer sequence':
+ self.primer_seq: str = str(s[1].strip())
+ elif s[0] == 'Function to evaluate internal priming':
+ self.priming_func: str = str(s[1].strip())
+ LOG.info("Parameters loaded.")
diff --git a/tests/resources/Param_test.txt b/tests/resources/Param_test.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6af6df2c32ab69c6a3d776a5cc0909a890bea1a0
--- /dev/null
+++ b/tests/resources/Param_test.txt
@@ -0,0 +1,27 @@
+Csv transcripts file: ./transcripts.csv
+
+Reference genome file: ./home/ref.ref
+
+Transcripts annotation file: ./home/annotations.ann
+
+Output folder: ./home/output
+
+Number of reads: 10023
+
+Number of cells: 34
+
+Average RNA fragments length: 150
+
+RNA fragment length standard deviation: 10
+
+Reads length: 100
+
+Intron retaining probability: 0.2
+
+Add poly A tail: TRUE
+
+Function to add poly A tail: generate_poly_a
+
+Primer sequence: ACCTGATCGTACG
+
+Function to evaluate internal priming: internal_priming
\ No newline at end of file
diff --git a/tests/test_parser.py b/tests/test_parser.py
new file mode 100644
index 0000000000000000000000000000000000000000..364ce9b8dfad69cf60749b7daf78e9c05c326667
--- /dev/null
+++ b/tests/test_parser.py
@@ -0,0 +1,25 @@
+"""Tests the parameter parser class."""
+
+import pytest
+from pathlib import Path
+from src import parameter_parser as pp
+from src import poly_a
+
+def test_parser():
+ """Tests the attributes of the class."""
+ par=pp.ParamParse('./tests/resources/Param_test.txt')
+ assert par.param_file == Path('./tests/resources/Param_test.txt')
+ assert par.transcripts_file == Path('./transcripts.csv')
+ assert par.genome_ref_file == Path('./home/ref.ref')
+ assert par.annotations_file == Path('./home/annotations.ann')
+ assert par.output_path == Path('./home/output')
+ assert par.n_reads == 10023
+ assert par.n_cells == 34
+ assert par.rna_avg == 150
+ assert par.rna_sd_length == 10
+ assert par.read_length == 100
+ assert par.intron_rate == 0.2
+ assert par.add_poly_a == bool('TRUE')
+ assert par.poly_a_func == 'generate_poly_a'
+ assert par.primer_seq == 'ACCTGATCGTACG'
+ assert par.priming_func == 'internal_priming'
\ No newline at end of file
diff --git a/tests/test_sampleinput.py b/tests/test_sampleinput.py
index f73dfb9dedc3d9436a585f75f356685f59e30e9a..3f81651fa79f0e6cedb59c24ec8322141870c9af 100644
--- a/tests/test_sampleinput.py
+++ b/tests/test_sampleinput.py
@@ -1,4 +1,4 @@
-"""Placeholder test for pipeline."""
+"""Tests the transcriptome abundance file input reader."""
import pytest
import pandas as pd