fix: flake8 fixes

transcript_structure/Generate_transcript_structure.py

+"""Creates differently spliced transcripts."""
+
 import random
 import csv
 import copy
 
 
 class BuildTranscriptStructure:
-
     """Creates differently spliced transcripts.
 
     Args:
@@ -34,7 +35,6 @@ class BuildTranscriptStructure:
         gtf_lines(list): List with all newly created gtf lines.
         _transcripts_generated(bool): Indicates whether splicing was conducted or not yet.
     """
-
     def __init__(self,
                  input_gene_count: str,
                  input_coordinates: str,
@@ -110,7 +110,7 @@ class BuildTranscriptStructure:
                 self.gene_sequences_dict[gene_name] = gene_info
 
     def _make_new_transcripts(self) -> None:
-        """ Generates the differently spliced transcripts."""
+        """Generates the differently spliced transcripts."""
         for gene in self.gene_count_dict:
 
             # Computes the intron splicing for each transcript.
@@ -136,7 +136,7 @@ class BuildTranscriptStructure:
             self.gene_transcript_dict[gene] = transcript_numbers
 
     def _make_gtf_info(self) -> None:
-        """ Writes the lines of the new gtf file for the differently spliced transcripts."""
+        """Writes the lines of the new gtf file for the differently spliced transcripts."""
         for gene in self.gene_transcript_dict:  # Iterates over all genes required.
             self.gtf_lines.append(self.gene_sequences_dict[gene]['gene_line'])  # Add gene line to list.
             sense = self.gene_sequences_dict[gene]['strand_sense']
@@ -189,12 +189,9 @@ class BuildTranscriptStructure:
                 self.gtf_lines.extend(exon_lines)
 
     def _sort_gtf_lines(self) -> None:
-
-        """ Sorts the gtf lines by the position of the genes (increasing) and returns it."""
-
+        """Sorts the gtf lines by the position of the genes (increasing) and returns it."""
         # Builds and uses a dictionary with the start of the gene as key, and all lines related to this gene as value:
         # {start_gene(int): [[gene_line],[transcript_line],[exon_line1],[exon_line2],...]}
-
         gene_lines_dict = {}
         gene_start = 0  # Validation: This key should remain unused, as every gtf file starts with a gene.
         for index, line in enumerate(self.gtf_lines):
@@ -214,13 +211,11 @@ class BuildTranscriptStructure:
     def write_csv(self,
                   csv_output: str
                   ) -> None:
-
-        """ Writes a csv file containing the number of differently spliced transcripts.
+        """Writes a csv file containing the number of differently spliced transcripts.
 
         Args:
              csv_output(str): Path and name of the output cvs file: "transcript_ID", "gene_ID", count.
         """
-
         with open(csv_output, 'w', newline='') as file:
             writer = csv.writer(file)
             writer.writerow(['Transcript_ID', 'Gene_ID', 'count'])
@@ -231,8 +226,7 @@ class BuildTranscriptStructure:
     def write_gtf(self,
                   gtf_output: str
                   ) -> None:
-
-        """ Writes a gtf file with the information about the differently spliced transcripts.
+        """Writes a gtf file with the information about the differently spliced transcripts.
 
         Args:
             gtf_output(str): Path and name of the output gtf file with the information of all relevant transcripts.
@@ -242,7 +236,7 @@ class BuildTranscriptStructure:
 
 
 def main():
-    """ Main Function."""
+    """Main Function."""
     # Inputs
     # gene_count = 'gene_count/Rik_5.csv'  # Strand with + sense
     # gene_count = 'gene_count/Rp1_5.csv'  # Strand with - sense.