From 55bd3a6572651e58cdd497a8ff27c6f1fa5ec823 Mon Sep 17 00:00:00 2001
From: Laura Urbanska <laura.urbanska@stud.unibas.ch>
Date: Tue, 10 Jan 2023 09:07:52 +0000
Subject: [PATCH] Deleted transcript_extractor.py (now part of find
representative transcript)
---
scripts/transcript_extractor.py | 329 --------------------------------
1 file changed, 329 deletions(-)
delete mode 100644 scripts/transcript_extractor.py
diff --git a/scripts/transcript_extractor.py b/scripts/transcript_extractor.py
deleted file mode 100644
index 5c81bcd..0000000
--- a/scripts/transcript_extractor.py
+++ /dev/null
@@ -1,329 +0,0 @@
-#### Transcript extractor #####
-"""Transcript extractor
-Version 1.2.0"""
-### Called Packages ###
-import re
-import os
-import time
-
-python_version = "3.7.13"
-module_list =[re,os,time]
-modul_name_list = ["re","os","time"]
-
-### Functions ###
-def version_control(module_list,modul_name_list,python_version):
- with open("required.txt","a") as req:
-
- for i in range(len(module_list)):
-
- try:
- version = module_list[i].__version__
- entry = modul_name_list[i]+"\t"+str(version)+"\n"
- req.write(entry)
- except:
- version = python_version
- entry = modul_name_list[i]+"\t"+str(version)+"\n"
- req.write(entry)
-
-def __parameter_editor(file_name,source_pathway_name,deposit_pathway_name):
- """This function allows for changing the parameters after running the program"""
- while True:
- print("The program will run with the following parameters:\nFile name:\t\t",file_name,"\nSource pathway:\t",source_pathway_name,"\nDeposit pathway:\t",deposit_pathway_name,"\n")
- parameter_conformation = input("To continue with these parameters input [continue or c] to change them input [edit]\n>")
- if parameter_conformation == "continue"or parameter_conformation =="c":
- break
- elif parameter_conformation == "edit":
- #edit the parameters
- while True:
- change_question = input("select the parameter you want to change [nfile/spath/dpath] or input [b] to go back\n>")
- if change_question == "nfile":
- #This condition allows the user to chenge the file name
- file_name = input("Please input the new file name\n>")
- break
- elif change_question == "spath":
- #This condition allows the user to change the source path
- source_pathway_name = input("Please input the new source path\n>")
-
- does_source_pathway_exist = os.path.exists(source_pathway_name)
- if does_source_pathway_exist:
- break
- else:
- print("The new source pathway:",source_pathway_name,"does not exist\nThe source pathway was returned to default:",os.getcwd())
- source_pathway_name = os.getcwd()
- elif change_question == "dpath":
- #This condition allows the user to change output file location
- deposit_pathway_name = input("Please input the new output file path name\n>")
- does_deposit_pathway_exist = os.path.exists(deposit_pathway_name)
- if does_deposit_pathway_exist:
- break
- else:
- print("The new deposit pathway:",deposit_pathway_name,"does not existe\nThe deposit pathway was returnt to default:",source_pathway_name)
- deposit_pathway_name = source_pathway_name
- #The block above test if the new deposit pathway is valid
- elif change_question == "b":
- # This condition allows the user to return to the main loop
- break
- else:
- #This condition covers all non valid inputs into the secund loop
- print("The input",change_question,"is not valid. Please use one of the specified commands")
-
- else:
- #This condition covers all non valid input for the main loop
- print("The input",parameter_conformation,"is not valide please use one of the specified comands\n")
- return(file_name,source_pathway_name,deposit_pathway_name)
-
-
-
-
-
-
-
-def __searche_for_preexisting_files(file_name,deposit_pathway_name = os.getcwd()):
- """This function searches for preexisting files of the same name as the results file of the current program. It allows the user to choose to move on with the pre-existing file """
- File_of_same_name_found = False
- generat_new_file = False
- directory_content = os.listdir(deposit_pathway_name)
- for file in directory_content:
- if file == file_name:
- while True:
- File_found_input = input (file_name+" has allready been generated\nDo you want to generate a new one [y/n] \n>")
- if File_found_input == "n":
- File_of_same_name_found = True
- break
- elif File_found_input == "y":
- generat_new_file = True
- break
- else:
- print("Invalid input\nPlease press [y] if you want to generate a new file or [n] if you want to use the preexisting file")
- break
- else:
- continue
- if File_of_same_name_found:
- print("No new file will be generated, the program can continue")
- elif generat_new_file:
- print("A new file will be generated please wait...\n")
- else:
- print("No pre-existing file of the relevant type has been found.\nA new file will be generated please wait...\n")
- return(File_of_same_name_found)
-
-def bar_builder(percentage = 0,length_multiplyer = 2,start_time = time.time(),bar = str()):
- """This function creates a loading bar that can load in 10% increments starting a 0% and ending at 100%
- Expected inputs:
- percentage: int between 0 and 100 in steps of 10; default = 0 #defines the current loading increment
- length_multiplyer: int > 0 ; default = 2 #determiens the amount of symbols per loading increment
- start_time: any int ; default= time.time() #for determening loading time
- bar: str ; default = str()#input of the current bar status does not need to be defined if for the 0% increment
- """
- if percentage == 100:
- bar = bar.replace("-","#")
- print("\r"+bar+"\t"+"100%\t\t"+str(int(time.time()-start_time)))
- elif percentage > 0:
- bar = bar.replace("-","#",length_multiplyer)
- print("\r"+bar+"\t"+str(percentage)+"%", end='',flush=True)
- elif percentage == 0:
- bar = "["+"-"*length_multiplyer*10+"]"
- print(bar+"\t", end='',flush=True)
- return(bar,start_time)
-
-def __test_file_name(file_name,source_pathway_name = os.getcwd()):
- """This function validates that the source file exists at the source path. It turns the file name input in a standardized format that can be used in the next steps"""
-
- directory_content = os.listdir(source_pathway_name)
-
- index_of_the_dot = file_name.rfind(".")
- valide_source_file = False
- validate_source_file = True
- if index_of_the_dot ==-1:
- file_name += ".gtf"
- else:
- source_file_typ = file_name[index_of_the_dot:]
- not_a_file_type = re.compile(".\d{1,13}")
- try_not_a_file_type = not_a_file_type.search(source_file_typ)
- if source_file_typ == ".gtf":
- file_name = file_name
- elif try_not_a_file_type:
- file_name += ".gtf"
- else:
- print("This program can not handle",source_file_typ,"files. \nplease use a .gtf file" )
- validate_source_file = False
- #The block above tests if the file_name includes the file type and if no
- #file type is found adds ".gtf" und if a non ".gtf" file is found gives an error
-
- if validate_source_file:
- for file in directory_content:
- if file == file_name:
- valide_source_file = True
- break
- #The block above tests if a file on the given name is in the given directora
-
- if valide_source_file:
- print("The file:",file_name,"has been found.\n")
- else:
- print("No .gtf file of the name",file_name,"has been found in this pathway")
- #The bock above gives feed back regarding the results of the file test
-
- file_name = file_name.replace(".gtf","")
- #This line normalizes the file name
- return(valide_source_file,file_name)
-
-def __do_pathways_exist__(source_pathway_name,deposit_pathway_name):
- """This funtion tests that the entered pathways actualy exist"""
- does_source_pathway_exist = os.path.exists(source_pathway_name)
- does_deposit_pathway_exist = os.path.exists(deposit_pathway_name)
- #The Block above does the actual testing
- if does_source_pathway_exist:
- source_pathway_name = source_pathway_name
- else:
- print("The source pathway:",source_pathway_name,"has not been found\nThe source pathway was set to the default")
- source_pathway_name = os.getcwd()
- #The block above detail the possible reactions for the source pathe existing or not existing
- if does_deposit_pathway_exist:
- deposit_pathway_name = deposit_pathway_name
- else:
- print("The deposit pathway:",deposit_pathway_name,"has not been found\nThe deposit pathway was set to the default")
- deposit_pathway_name = source_pathway_name
- #The block above details the possible reactions for the deposit pathway existing or not existing
- return(source_pathway_name,deposit_pathway_name)
-
-def gene_ID_finder(entry):
- """This function is supposed to find the gene ID of a known gene entry
- Expected inputs:
- entry: str #a line from a gtf file that contains a gene ID"""
- index_gene_id = entry.find("gene_id")
- find_gene_id_name = re.compile("\"\S{1,25}\"")
- sub_entry = entry[index_gene_id:]
- try_find_gene_id_name = find_gene_id_name.search(sub_entry)
- gene_ID = try_find_gene_id_name[0].replace("\"","")
- return (gene_ID)
-
-def transcript_ID_finder (entry):
- """This function is supposed to finde the transcript ID in a known transcript entry
- Expected inputs:
- entry: str #a line from a gtf file that contains a transcript ID"""
- 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)
-
-def transcript_support_level_finder(entry):
- """This function is supposed to find the transcript support level in a known transcript entry
- Expected input:
- entry: str #a line from a gtf file that be blongs to a transcript"""
- transcript_support_level_start_ID = entry.find("transcript_support_level")
- sub_entry = entry[transcript_support_level_start_ID:]
-
- try:
- score_finder = re.compile("\W\w{1,16}\W{2}")
- try_score_finder = score_finder.search(sub_entry)
- Pre_score_1 = try_score_finder[0]
- Pre_score_2 = Pre_score_1.replace("\"","")
- Pre_score_2 = Pre_score_2.replace("(","")
- transcript_support_level = Pre_score_2.replace(";","")
- if "NA" in transcript_support_level:
- transcript_support_level = 100
- #I changed This tell laura
-
-
- except:
- transcript_support_level = 100
- return (transcript_support_level)
-
-
-
-
-def _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name):
- """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"""
-
- with open(os.path.join(source_pathway_name,file_name+".gtf"), 'r') as f:
- total_entrys =len(f.readlines())
- with open(os.path.join(source_pathway_name,file_name+".gtf"), 'r') as f:
- current_entry = 0
- percentage_done = 0
- bar,start_time = bar_builder(length_multiplyer = 3)
-
-
- Old_gen_ID = str()
- #stand-in as the first couple entrys are not genes
- with open(os.path.join(deposit_pathway_name,file_name+"_"+"intermediate_file"+".txt"),"w") as IMF:
- transcript_number = 0
- for entry in f:
-
-
- current_entry += 1
- current_percentage_done = 100* current_entry/total_entrys
- if current_percentage_done > percentage_done +10:
- bar,start_time = bar_builder(percentage=percentage_done+10,length_multiplyer = 3,start_time=start_time,bar =bar)
- percentage_done = int(current_percentage_done)
-
- if "gene_id" in entry:
- Gen_ID = gene_ID_finder(entry)
- else:
- Gen_ID = Old_gen_ID
-
- if Gen_ID != Old_gen_ID:
- Gen_entry = ">"+ Gen_ID +"\n"
- IMF.write(Gen_entry)
- transcript_number = 0
- Old_gen_ID = Gen_ID
-
- if "\ttranscript\t" in entry:
- transcript_number += 1
- Transcript_ID = transcript_ID_finder(entry)
- #the function that determins the transcript ID is called
- transcript_support_level = transcript_support_level_finder(entry)
- #the function that determins the transcript support level is called
- New_entry = str(transcript_number)+"\t"+str(Transcript_ID)+"\t"+str(transcript_support_level)+"\t"+"\t\n"
- IMF.write(New_entry)
- bar_builder(100,length_multiplyer = 3,start_time=start_time,bar =bar)
- print("The transcripts have been collected")
-
-
-def extract_transcript(file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name = False,Input_free = False):
- """ This it the overall exetutable funtion that will execute the transcript extraction process for a given file with all checks.
- Expected input:
- 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 = source_pathway_name #path for saving the intermediat file
- Outputs:
- file_name: str
- source_pathway_name: str
- deposit_pathway_name: str
- """
-
-
- if deposit_pathway_name == False:
- deposit_pathway_name = source_pathway_name
- if Input_free:
- validated_file_name = __test_file_name(file_name,source_pathway_name)
- file_name = validated_file_name[1]
- _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name)
- else:
- file_name,source_pathway_name,deposit_pathway_name = __parameter_editor(file_name,source_pathway_name,deposit_pathway_name)
- source_pathway_name,deposit_pathway_name =__do_pathways_exist__(source_pathway_name,deposit_pathway_name)
- validated_file_name = __test_file_name(file_name,source_pathway_name)
- file_name = validated_file_name[1]
- if validated_file_name[0]:
- if __searche_for_preexisting_files(file_name+"_intermediate_file.txt",deposit_pathway_name):
- print("The transcripts has been collected\n")
- else:
- _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name)
- return(file_name,source_pathway_name,deposit_pathway_name)
-
-#### Dev part ####
-
-if __name__ == "__main__":
- #version_control(module_list,modul_name_list,python_version)
- extract_transcript()
-#This line allows the file to be executed on its own also from
-
-
--
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