Deleted exon_length_filter.py (redundant)

scripts/exon_length_filter.py

-#### Exon length filter #####
-"""Exon length filter 
-Version 2.1.0"""
-### Called Packages ###
-import re
-import os
-
-import transcript_extractor as te
-
-python_version = "3.7.13"
-module_list =[re,os]
-modul_name_list = ["re","os"]
-
-### Functions ###
-
-def exon_length_calculator(entry): 
-    """This function finds the start and end cordinates of the exon and uses them to calculate its length"""
-    try:
-        find_exon_coordinates = re.compile("\t\d{1,15}\t")
-        #this difines the pattern of the coordinates 
-        try_find_start_coordinates = find_exon_coordinates.search(entry)
-        #this line findes the start coordinares based on the pattern 
-        start_coordinates = int(try_find_start_coordinates[0].replace("\t",""))
-        #this line removes the \t at the end and the start of the pattern and 
-        #turn the string of the coordinates into intergers  
-        final_index_start_coordinates = entry.find(try_find_start_coordinates[0])+len(try_find_start_coordinates[0])-1
-        #this line determines the indes of the final digit of the start coordinates    
-        sub_entry = entry[final_index_start_coordinates:]
-        #this lineused the index determin above a starting point for a new sub entry
-        try_find_end_coordinates = find_exon_coordinates.search(sub_entry)
-        end_coordinates = int(try_find_end_coordinates[0].replace("\t",""))
-        #these two lines find the end coordinates and turn tham int an int 
-        exon_length = end_coordinates-start_coordinates
-        #this line claculates the transcript length 
-    except:
-        print("\n\nIn the following enty only one or no valid coordinates could be found:\n",entry,"the value will be set to NA")
-        exon_length = "NA"
-    return(exon_length)
-
-def exon_fider(entry):
-    """This funtion determines if a given entry belongs to an exon
-    Expected inputs:
-        entry: str #any enty of a gtf file"""
-    exon_test = entry.find("\texon\t")
-    #This line look for the entry exon in the file
-    if exon_test == -1: 
-        try_exon_test = False
-    else:
-        try_exon_test = True
-    #The block above evaluates the results of the search for the wort exon
-    return(try_exon_test)
-
-def __longest_transcript_finder(current_exon_length,longest_transcript,longest_transcript_ID,old_transcript_ID):
-    """This funtion encapsulates an operation that has to be carried out at several points in the exon_length_filter function and serves to make that function more modular"""
-    if current_exon_length > longest_transcript: 
-        #This condition updates the most promesing for
-        #beeing the representative transcript
-        longest_transcript = current_exon_length
-        longest_transcript_ID = old_transcript_ID
-    current_exon_length = 0
-    return(current_exon_length,longest_transcript,longest_transcript_ID)
-
-def _representative_transcript_csv (representative_transcript,file_name = "test",deposit_pathway_name =os.getcwd()):
-    with open(os.path.join(deposit_pathway_name,file_name+"_"+"representative_transcripts"+".csv"),"w") as rt:
-        for i in representative_transcript:
-            transcript = representative_transcript[i]
-            new_entry = str(i)+","+transcript+"\n"
-            rt.write(new_entry)
-    
-
-        
-def _exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name =os.getcwd(),gen_dict = {"ENSG00000160072":["ENST00000673477","ENST00000472194","ENST00000378736","ENST00000308647","ENST00000442483"],"ENSG00000225972":["ENST00000416931"],"ENSG00000279928":["ENST00000624431","ENST00000424215"],"ENSG00000142611":["ENST00000378391","ENST00000607632","ENST00000511072"]}):
-    """This funtion selects only the transcripts for a dictionary that have the longest total mRNA"""  
-    bar,start_time = te.bar_builder(length_multiplyer = 3)
-    total_genes = len(gen_dict)
-    gens_done = 0
-
-    with open(os.path.join(source_pathway_name,file_name+".gtf"), 'r') as f:
-        
-        old_gen = str()
-        old_transcript_ID = str()
-        representative_transcript = dict()
-        representative_trasnscript_not_found = True
-        longest_transcript_ID = str()
-        current_exon_length = 0
-        longest_transcript = 0 
-        percentage_done = 0
-        
-        for entry in f: 
-            
-            try:
-                corrent_gen = te.gene_ID_finder(entry)
-            except:
-                corrent_gen = old_gen
-            #The block above test if there is a gen name in the entry
-            if corrent_gen != old_gen:   
-                representative_trasnscript_not_found = True
-
-            #The block above determines if the Gen name is new and set the test
-            #representative_trasnscript_not_found back to true which is used to 
-            #make the program faster if there is just one transcript for a given
-            #gen in the dict
-            if representative_trasnscript_not_found and corrent_gen != str():
-                #print(corrent_gen)
-                #The conditon prvents serges if a representative transcript has
-                #all ready been chosen
-                if corrent_gen != old_gen:
-                    current_exon_length,longest_transcript,longest_transcript_ID = __longest_transcript_finder(current_exon_length,longest_transcript,longest_transcript_ID,old_transcript_ID)
-                    representative_transcript[old_gen] = longest_transcript_ID
-                    try:
-                        del gen_dict[old_gen]
-                        old_gen = corrent_gen                   
-                        gens_done += 1
-                        corrent_percentage_done = (gens_done/total_genes)*100
-                        if corrent_percentage_done > percentage_done+10:
-                            bar,start_time = te.bar_builder(percentage=percentage_done+10,length_multiplyer = 3,start_time=start_time,bar =bar)
-                            percentage_done = int(corrent_percentage_done)  
-                        
-                         
-                    except:
-                        old_gen = corrent_gen
-                    longest_transcript = 0
-                    #The block above adds the transcript of the last gen that 
-                    #had the longest exons into the representative transcripts dict
-                    try: 
-                        #This try / except block test if the gen is in the input dictionary
-                        transcript_IDs = gen_dict[corrent_gen]
-                        if len(gen_dict[corrent_gen]) == 1:
-                            #This conditions is a short cut for Genes that 
-                            #allready have a representative transcript
-                            representative_transcript=gen_dict[corrent_gen[0]]
-                            representative_trasnscript_not_found = False
-                            continue
-                    except:
-                        continue
-                    
-                try: 
-                    current_transcript_ID = te.transcript_ID_finder(entry)         
-                except: 
-                    continue
-                #The block above searches for a transcript ID in the current entry
-
-                if current_transcript_ID in transcript_IDs:
-                    #This condition test if the Transcript is one of the 
-                    #candidates for representative transcripts
-                    if current_transcript_ID != old_transcript_ID:
-                        #This condition if the enty still belongs to the 
-                        #previous transcript and is triggers if that is not the case
-                        current_exon_length,longest_transcript,longest_transcript_ID = __longest_transcript_finder(current_exon_length,longest_transcript,longest_transcript_ID,old_transcript_ID)
-                        try:
-                            transcript_IDs.remove(old_transcript_ID)
-                            old_transcript_ID = current_transcript_ID
-                        except:
-                            old_transcript_ID = current_transcript_ID
-                    if exon_fider(entry): 
-                        exon_length = exon_length_calculator(entry)
-                        current_exon_length += exon_length
-                    else: 
-                        continue 
-        current_exon_length,longest_transcript,longest_transcript_ID = __longest_transcript_finder(current_exon_length,longest_transcript,longest_transcript_ID,old_transcript_ID)
-        representative_transcript[old_gen] = longest_transcript_ID
-    del representative_transcript[str()]
-    te.bar_builder(100,length_multiplyer = 3,start_time=start_time,bar =bar)
-    return(representative_transcript)
-
-def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name =os.getcwd(),gen_dict = {"ENSG00000160072":["ENST00000673477","ENST00000472194","ENST00000378736","ENST00000308647","ENST00000442483"],"ENSG00000225972":["ENST00000416931"],"ENSG00000279928":["ENST00000624431","ENST00000424215"],"ENSG00000142611":["ENST00000378391","ENST00000607632","ENST00000511072"]}):   
-    """This function filters a dictionary of genes and there transcripts by the length of there exons an selects the longes transcript for each gene and returns an dictionary {gene_ID : transcript_ID}.
-    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 files
-        gen_dict:dict{key == gene ID:[transcript IDs that belong to that gene]}""" 
-    
-    print("Representative trascipts are filterd based on exon length please wait...")
-    source_pathway_name,deposit_pathway_name = te.__do_pathways_exist__(source_pathway_name,deposit_pathway_name)
-    representative_transcript = _exon_length_filter(file_name,source_pathway_name,deposit_pathway_name,gen_dict)
-    print("\nRepresentative transcripts collected")
-    return(representative_transcript)
-    
-
-if __name__ == "__main__":
-    #te.version_control(module_list,modul_name_list,python_version)
-    exon_length_filter()
-    
-    
-#This line allows the file to be executed on its own also from