reformatted with black

cdna/cdna.py

 import sys
 
+
 def translate(res):
-    translate_dict = {"A": "T", "U": "A", "G": "C", "C":"G"}
+    translate_dict = {"A": "T", "U": "A", "G": "C", "C": "G"}
     if res not in translate_dict.keys():
         print("cDNA residue not A,T,U or G ")
         sys.exit(1)
     return translate_dict[res]
 
+
 class cDNA_Gen:
-    def __init__(self, 
-                 fasta, 
-                 gtf, 
-                 cpn, 
-                 output_fasta = "cDNA.fasta",
-                 output_csv = "cDNA.csv"
-                ):
+    def __init__(
+        self, fasta, gtf, cpn, output_fasta="cDNA.fasta", output_csv="cDNA.csv"
+    ):
         # inputs
         self.fasta = fasta
         self.gtf = gtf
@@ -26,27 +24,25 @@ class cDNA_Gen:
         self.fasta_seq = ""
         self.fasta_id = ""
         self.copy_numbers = {}
-        
+
         self.run()
-        
+
     def run(self):
         self.read_fasta()
         self.read_gtf()
-        
+
     def order_priming_sites(self):
         pass
-    
+
     def generate_cdna(self):
         pass
-    
-    
+
     def read_fasta(self):
         fasta = open(self.fasta).readlines()
         self.fasta_id = fasta[0]
         print(fasta[0])
         self.fasta_seq = "".join([_.rstrip() for _ in fasta[1:]])
-        
-    
+
     def read_gtf(self):
         with open(self.gtf) as gtf_file:
             gtf_lines = gtf_file.readlines()
@@ -58,7 +54,7 @@ class cDNA_Gen:
 
     def write_fasta(self):
         pass
-    
+
     def read_copy_numbers(self):
         with open(self.cpn) as cpn_file:
             cpn_lines = cpn_file.readlines()
@@ -69,11 +65,10 @@ class cDNA_Gen:
                     gene_id = csv[1]
                     count = csv[2]
                     self.copy_numbers[gene_id] = count
-                
-    
+
     def return_output(self):
         return self.output_fasta, self.output_csv
-    
+
 
 class GTF_entry:
     def __init__(self, string):
@@ -82,19 +77,18 @@ class GTF_entry:
         self.id = self.values[0]
         self.start = int(self.values[3])
         self.end = int(self.values[4])
-        self.score = float(0.5) #self.values[5]
+        self.score = float(0.5)  # self.values[5]
         self.sequence = "no sequence set"
         self.length = self.end - self.start
-        
+
     def __repr__(self):
         return self.sequence[:10] + "..." + f" len={self.length} score={self.score}"
-    
+
     def set_sequence(self, full_sequence):
-        self.sequence = full_sequence[self.start:self.end]
-    
-    
+        self.sequence = full_sequence[self.start : self.end]
+
+
 if __name__ == "__main__":
     import argparse
+
     pass
-    
-