Merge branch 'feature_max' into 'main'

CreatePrimer class and preprocessing module

See merge request !20

primingsitepredictor/Primer1.fasta

+<primer1
+TTTTTTTTTTTTTTT

primingsitepredictor/cli.py

@@ -8,6 +8,7 @@ import argparse
 import logging
 
 def create_parser():
+    """This function creates the parser"""
     parser = argparse.ArgumentParser(
     prog = 'Priming site predictor',
     description = 'Takes a cutoff energy and the predicts location of priming sites of transcripts',

primingsitepredictor/createprimer.py

+# -*- coding: utf-8 -*-
+"""
+Created on Wed Nov 16 14:17:06 2022
+
+@author: baerma
+"""
+
+class CreatePrimer:
+    """This Class creates an instance of a primer of a desired length and primer name
+    which can be saved as a fasta file. By default the length is 15 and name is primer1"""
+    def __init__(self, name='primer1', primerlength=15):
+        self.name = name
+        self.primer_length = primerlength
+        self.primer_sequence = 'T'*self.primer_length
+        self.lines = [f'<{self.name}', self.primer_sequence]
+        #print(self.primer)
+        #return self.primer
+    
+    def create_fasta(self):
+        with open(f'{self.name}.fasta', 'w') as f:
+            for line in self.lines:
+                f.write(line)
+                f.write('\n')
+
+
+
+

primingsitepredictor/preprocessingmodule.py

+# -*- coding: utf-8 -*-
+"""
+Created on Wed Nov 16 14:17:06 2022
+
+@author: baerma
+"""
+from createprimer import CreatePrimer
+
+def generate_RIBlast_input():
+    """This function creates a list of the filenames for the RIBlast"""
+    my_primer = CreatePrimer()
+    my_primer.create_fasta()
+    primer_filename = my_primer.name +".fasta"
+    transcripts_filename = "transcripts.fasta"
+    
+    return [primer_filename, transcripts_filename]
+
+print(generate_RIBlast_input())
+
+
+