From 1d5a1253af0ac18b9ed0e26ccdd5ef2ab6a6365c Mon Sep 17 00:00:00 2001
From: LauraU123 <laura.urbanska@stud.unibas.ch>
Date: Fri, 11 Nov 2022 10:00:35 +0100
Subject: [PATCH] fixed typos and new version of trancript extractor
---
scripts/exon_length_filter.py | 31 +--
...t_extractor.py => transcript_extractor.py} | 207 +++++++++---------
2 files changed, 108 insertions(+), 130 deletions(-)
rename scripts/{trancript_extractor.py => transcript_extractor.py} (67%)
diff --git a/scripts/exon_length_filter.py b/scripts/exon_length_filter.py
index 4ccc8a9..2ebfb4f 100644
--- a/scripts/exon_length_filter.py
+++ b/scripts/exon_length_filter.py
@@ -3,7 +3,6 @@
### Called Packages ###
import re
import os
-import time
import transcript_extractor as te
### Functions ###
@@ -12,42 +11,30 @@ def exon_length_calculator(entry):
"""This funtion finds the start and end cordinates of the exon and uses them to calculate its lenght"""
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
+ final_index_start_coordinates = entry.find(try_find_start_coordinates[0])+len(try_find_start_coordinates[0])-1
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_lenght = end_coordinates-start_coordinates
- #this line claculates the transcript length
+ exon_length = end_coordinates-start_coordinates
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_lenght = "NA"
- return(exon_lenght)
+ exon_length = "NA"
+ return(exon_length)
def exon_fider(entry):
"""This funtion determines if a given entry belongs to an exon"""
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 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 encapsulates an operation that has to be carried out multiple times in the exon_length_filter"""
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
@@ -56,9 +43,9 @@ def __longest_transcript_finder(current_exon_length,longest_transcript,longest_t
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 dictionar that have the longest total mRNA"""
+ """This function selects only the transcripts that have the longest total mRNA"""
- print("Representative trascipts are filterd based on exon length please wait...")
+ print("Representative transcipts are filtered based on exon length. Please wait...")
bar,start_time = te.bar_builder(length_multiplyer = 3)
source_pathway_name,deposit_pathway_name = te.__do_pathways_exist__(source_pathway_name,deposit_pathway_name)
total_genes = len(gen_dict)
@@ -127,7 +114,7 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
current_transcript_ID = te.transcript_ID_finder(entry)
except:
continue
- #The block above searches for a trnascript ID in the current enty
+ #The block above searches for a transcript ID in the current enty
if current_transcript_ID in transcript_IDs:
#This condition test if the Transcript is one of the
@@ -155,5 +142,3 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
if __name__ == "__main__":
exon_length_filter()
-
-#This line allows the file to be executed on its own also from
diff --git a/scripts/trancript_extractor.py b/scripts/transcript_extractor.py
similarity index 67%
rename from scripts/trancript_extractor.py
rename to scripts/transcript_extractor.py
index 054b92f..1b901a7 100644
--- a/scripts/trancript_extractor.py
+++ b/scripts/transcript_extractor.py
@@ -3,8 +3,64 @@
### Called Packages ###
import re
import os
+import time
### Functions ###
+
+
+
+def __parameter_editor(file_name,source_pathway_name,deposit_pathway_name):
+ """This function allows for chaging 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 """
@@ -23,7 +79,7 @@ def __searche_for_preexisting_files(file_name,deposit_pathway_name = os.getcwd()
generat_new_file = True
break
else:
- print("Sorry this was not a valid input\nPlease press [y] if you want to generate a new file or [n] if you want to use the preexisting file")
+ 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
@@ -35,6 +91,18 @@ def __searche_for_preexisting_files(file_name,deposit_pathway_name = os.getcwd()
print("No pre-existing intermediate file based on the currend file have 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()):
+ 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"""
@@ -96,31 +164,23 @@ def __do_pathways_exist__(source_pathway_name,deposit_pathway_name):
return(source_pathway_name,deposit_pathway_name)
def gene_ID_finder(entry):
- """This function is supposed to finde the gen ID of a known gen entry"""
+ """This function is supposed to find the gene ID of a known gene entry"""
index_gene_id = entry.find("gene_id")
- #This line determines where the transcript ID is
find_gene_id_name = re.compile("\"\S{1,25}\"")
- #This line defines the pattern of a transcript ID
sub_entry = entry[index_gene_id:]
- #This line generates a subentra starting at the locatind of the tanscript ID
try_find_gene_id_name = find_gene_id_name.search(sub_entry)
gene_ID = try_find_gene_id_name[0].replace("\"","")
- #The block above findes the transcript ID and changes it into a usable format
return (gene_ID)
def transcript_ID_finder (entry):
"""This function is supposed to finde the transcript ID in a known transcript entry"""
index_transcript_id = entry.find("transcript_id")
- #This line determines where the transcript ID is
find_transcript_id_name = re.compile("\"\S{1,25}\"")
- #This line defines the pattern of a transcript ID
sub_entry = entry[index_transcript_id:]
- #This line generates a subentra starting at the locatind of the tanscript ID
try_find_transcript_id_name = find_transcript_id_name.search(sub_entry)
try:
transcript_ID = try_find_transcript_id_name[0].replace("\"","")
- #The block above findes the transcript ID and changes it into a usable format
except:
transcript_ID = ""
return (transcript_ID)
@@ -131,19 +191,18 @@ def transcript_support_level_finder(entry):
sub_entry = entry[transcript_support_level_start_ID:]
try:
- #the try and except clauses are there for the case that there is
- #no actual score given
- score_fidner = re.compile("\W\w{1,16}\W{2}")
- try_score_finder = score_fidner.search(sub_entry)
+ 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 transcript_support_level == "NA":
+ if "NA" in transcript_support_level:
transcript_support_level = 100
+ #I changed This tell laura
+
except:
- #will give NA if no numerical score is found
transcript_support_level = 100
return (transcript_support_level)
@@ -151,121 +210,55 @@ def transcript_support_level_finder(entry):
def _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name):
- """This funtion 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 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"""
+ with open(source_pathway_name+"\\"+file_name+".gtf", 'r') as f:
+ total_entrys =len(f.readlines())
with open(source_pathway_name+"\\"+file_name+".gtf", 'r') as f:
- #this line opens the file in question
+ 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(deposit_pathway_name+"\\"+file_name+"_"+"intermediat_file"+".txt","w") as IMF:
- #creates a new file that will have the same name as the source file
- #but with an added _inter_mediat_file
+ with open(deposit_pathway_name+"\\"+file_name+"_"+"intermediate_file"+".txt","w") as IMF:
transcript_number = 0
for entry in f:
- #this loop reads all lines in the source file one by one
- Gen_finder = re.compile("gene_id")
- try_gen_finder = Gen_finder.search(entry)
- #the lines above determin if the is a "gene_name" collumn
- #in the current entry
- if (try_gen_finder):
+
+
+ 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
- #determins the gene_name using the function showen futher up
+
if Gen_ID != Old_gen_ID:
- #chachs if the gene is new or if it is an entry belonging
- #to the previous gen e.g. a transkript, exon ...
- Gen_entry = ">"+str(Gen_ID)+"\n"
+ Gen_entry = ">"+ Gen_ID +"\n"
IMF.write(Gen_entry)
- #if the Gen is new a new line is inserted in the intermediat
- #file to seperate the transcripts belonging to the different genes
transcript_number = 0
- #the transcript number indicates how many transcripts have
- #been found of the same gene befor the current one it starts
- #at 1 for each new gene
Old_gen_ID = Gen_ID
- #the new_name is set as the Old meaning current name
- transkript_finder = re.compile("\ttranscript\t")
- try_transkript_finder = transkript_finder.search(entry)
- #the lines above serve to identify if the current entry blonges
- #to a transcript
-
- if try_transkript_finder:
- #this confition is activated if the entry belongs to a transcript
+ if "\ttranscript\t" in entry:
transcript_number += 1
- #the transcript number is updated (starting at on given that t
- #he default is 0)
- Transcript_ID = transcript_ID_finder (entry)
+ 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)
- #this lines assemble the transcript number ,transcript ID
- #and the transcript support level into a new line for the
- #intermediat file and adds them in
- print("The transcripts have been collected")
+ bar_builder(100,length_multiplyer = 3,start_time=start_time,bar =bar)
+ print("The transcripts have been collected")
-def __parameter_editor(file_name,source_pathway_name,deposit_pathway_name):
- """This funtion allows for chaging the parameters after running the program"""
- while True:
- #This is the main loot wich allows show the current partameters and
- #allows the usert to shouse if the want to use edit the paremeters or
- #to continue with the given parameters
- 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>")
- #The block above incluts the "table" whith the current parameters as well as the input prompt
- if parameter_conformation == "continue"or parameter_conformation =="c":
- #This if clause will end the main loop and the funtion
- break
- elif parameter_conformation == "edit":
- #This conditin lead into the secundary loop which allows the user to 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>")
- #This is the input prompt for the secundary loop
- if change_question == "nfile":
- #This condition allows the user to chenge the file name
- file_name = input("Pleas 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("Pleas 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 existe\nThe source pathway was returnt to default:",os.getcwd())
- source_pathway_name = os.getcwd()
- #The block above test that if the new source pathway is valid
- elif change_question == "dpath":
- #This condition allows the user to change the deposit path
- deposit_pathway_name = input("Pleas input the new deposit 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 valide please use one of the specifyed comands")
-
- 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 specifyed comands\n")
- return(file_name,source_pathway_name,deposit_pathway_name)
-def extract_transkript (file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name = False):
+def extract_transkript (file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name = True):
"""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"""
- if deposit_pathway_name == False:
+ if deposit_pathway_name and type(deposit_pathway_name) != str :
deposit_pathway_name = source_pathway_name
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)
--
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