"""This function encapsulates an operation that has to be carried out multiple times in the exon_length_filter"""
"""This funtion encapsulates an opperation that has to be carried out at several point ind the exon_length_filter funktion and servers to make that funktion more modular"""
"""This function filters a dictionary of genes and there transcripts by the length of there exons an selects the longes transcript for each gene ans saves tham in a "," seperated csv file.
Expected inputs:
file_name: str ; default = test #the name of the gft file you want to look at
source_pathway_name: str ; default = current work directory #path of the gtf file
deposit_pathway_name: str ; default = current work directory #path for saving the csv file
gen_dict:dict{key == gene ID:[transcript IDs that belong to that gene]}
Input_free: tuple ; default = False # this input should be set to True for automation"""
print("Representative trascipts are filterd based on exon length please wait...")
"""This functi extracts the transcript number ,transcript ID, the transcript support level, the transcrip length and the line index from a gtf file of a given name and saves tham as a new file name given_name_intermediat_file.txt. It only works in the directory of the skript at this point"""
"""This function extracts the transcript number ,transcript ID, the transcript support level, the transcrip length and the line index from a gtf file of a given name and saves tham as a new file name given_name_intermediat_file.txt.
Expected input:
file_name: str #the name of the gft file you want to look at without the .gtf part
source_pathway_name: str #path of the gtf file
deposit_pathway_name: str #path for saving the intermediat file"""
"""This it the overall exetutable funtion that will execute the transcript extraction process for a given file with all checks.
The default file name is "test". This function will also return the file name, the source pathway and the depisti pathway that have been used to generate the intermediat file"""
