Deleted writegtf.py (now included in find representative transcript)

scripts/writegtf.py

-### Called Packages ###
-import pandas as pd
-import numpy as np
-import argparse
-import re
-
-import transcript_extractor as te
-
-python_version = "3.7.13"
-module_list =[pd,np,argparse,re]
-modul_name_list = ["pd","np","argparse","re"]
-### Functions ###
-
-def transcript_ID_finder (entry):
-    index_transcript_id = entry.find("transcript_id")
-    find_transcript_id_name = re.compile("\"\S{1,25}\"")
-    sub_entry = entry[index_transcript_id:]
-    try_find_transcript_id_name = find_transcript_id_name.search(sub_entry)   
-    
-    try: 
-        transcript_ID = try_find_transcript_id_name[0].replace("\"","")
-    except:
-        transcript_ID = ""
-    return (transcript_ID)
-
-
-'''gtf_file_writer takes as input the original gtf file and the csv file containing relevant transcripts.
-
-    It produces a gtf file containing only the transcript entries of those contained in the csv file
-    
-    based on id'''
-
-
-def gtf_file_writer (original_file, csv_file, output_file): 
-    output = []
-
-    df = pd.read_csv(csv_file)
-    listoftranscripts = df['id'].tolist()
-    if df['id'].empty:
-        print('Error. \'id\' column needed in input csv file.')
-
-    with open(original_file, 'r') as f:
-            for entry in f: 
-                if "\ttranscript\t" in entry:
-                    transcript_id = transcript_ID_finder(entry)
-                    if transcript_id in listoftranscripts:
-                        output.append(entry)
-    with open(output_file, 'w') as last_file:
-        for line in output : # I had to add this loop because I had an error about you cannot write list in directly in a file
-            last_file.write(line)
-
-
-if __name__ == '__main__':
-    te.version_control(module_list,modul_name_list,python_version)
-    parser = argparse.ArgumentParser(
-        description="gtf output file writer",
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter
-    )
-    parser.add_argument("--annotation", required=True, help="gtf file with genome annotation")
-    parser.add_argument("--output_gtf", required=True, help="output gtf file")
-    parser.add_argument("--input_csv", required=True, help="input csv file")
-    args = parser.parse_args()
-
-    gtf_file_writer(args.annotation, args.input_csv, args.output_gtf)