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Commit 55bd3a65 authored by Laura Urbanska's avatar Laura Urbanska
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Deleted transcript_extractor.py (now part of find representative transcript)

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#### 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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