Skip to content
Snippets Groups Projects
Commit e1f9cf86 authored by Laura Urbanska's avatar Laura Urbanska
Browse files

added trancript extractor script

parent 4b810197
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
scripts/representativeTranscript.py deleted 100644 → 0
+ 0
− 84
View file @ 4b810197
import pandas as pd
import re
'''
This part of the code find a representative transcript for each ID given in the csv input file.
It works with the output of the function "transcript selector".
It return a csv file containing the names of the representative transcript and their levels.
'''
#import csv file [ID, Expression_level] and create a df
def import_csv_to_df(csv_file) :
df_csv = pd.read_csv(csv_file, names=["ID", "Expression_level"])
return df_csv
#import modified gtf file and create a df
def import_gtfSelection_to_df(gtf_modified_file):
#create a df from the tab separated file input
df_input =pd.read_csv(gtf_modified_file, sep='\t', lineterminator='\n',
names =["Gene_mixed", "Transcript", "Support_level", "Length", "Line_index", "Na"] )
#Create a new column with only gene name from Gene_mixed column
df_input["Gene"] = df_input["Gene_mixed"].str.extract('([A-Z]\w{0,})', expand=True)
#Create a new column with only transcript number from Gene_mixed column
df_input["Transcript_number"] = df_input["Gene_mixed"].str.extract('(^\d)', expand=True)
#Create a new df with relevant column and without NA
df_clean = df_input.loc[:, ["Gene","Transcript_number","Transcript","Support_level", "Length", "Line_index"]]
df_clean["Gene"] = df_clean["Gene"].fillna(method='ffill')
df_clean = df_clean.dropna(axis=0)
return df_clean
# Return a df containing representative transcripts and their expression level from genes mentioned in the csv file
def representative_from_gene(df_gtfSelection, df_csv):
#check wich genes are shared by df_gtfSelection and df_csv and create a reduced df
df_shared = df_gtfSelection[(df_gtfSelection["Gene"].isin(df_csv["ID"]))]# /!\ return an empty list if I do the same with "Transcript" column.
#pick only the transcripts with the highest support level (best is = 1 )
df_filtered = df_shared[df_shared["Support_level"]==df_shared["Support_level"].min()]
#pick the transcript with the greatest length if multiple transcript have the same support level
df_filtered2 = df_filtered.sort_index().groupby(df_filtered["Gene"]).max()
#combine expression level with transcript with highest support level and greatest length
df_filtered2["Expression_level"] = df_filtered2.Gene.map(df_csv.set_index("ID")['Expression_level'])
#create a reduced df with only the representative transcript and its support level
df_final = df_filtered2[["Transcript","Expression_level"]]
print("This is your representative transcripts : \n \n {}".format(df_final))
return df_final
#Missing conditions :
# If multiple transcript form the same gene, add their expression
# If given transcript name, return the most representative transcript
# Output csv file containing representative transcript levels and id
def write_csv_Transcript_Expression_level(df_representative):
df_final = df_representative[["Transcript","Expression_level"]]
with open("transcripts.csv", "w") as fileout :
fileout.write(df_representative.to_csv(columns=["Transcript","Expression_level"], index=False))
### put your inputs here ! ###
ID_levels_csv = "scRNA\input.csv" # put your csv file here
gtf_file = "scRNA/test_inter_mediat_file.txt" # put your gtf selected file here
df_gtf = import_gtfSelection_to_df(gtf_file)
df_csv_input = import_csv_to_df(ID_levels_csv)
representative_transcript = representative_from_gene(df_gtf, df_csv_input)
write_csv_Transcript_Expression_level(representative_transcript) # create a csv file named "transcript.csv"
scripts/transkript_extractor.py 0 → 100644
+ 287
− 0
View file @ e1f9cf86
#### Transcript extractor #####
### Called Packages ###
import re
import os
### Functions ###
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:
Search_profile = file_name+"_intermediat_file.txt"
if file == Search_profile:
while True:
File_found_input = input ("An intermediate file has allready been generated from this file\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("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")
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 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 __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 finde the gen ID of a known gen 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)
def transcript_support_level_finder(entry):
"""This function is supposed to find the transcript support level in a known transcript entry"""
transcript_support_level_start_ID = entry.find("transcript_support_level")
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)
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":
transcript_support_level = 100
except:
#will give NA if no numerical score is found
transcript_support_level = 100
return (transcript_support_level)
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"""
with open(source_pathway_name+"\\"+file_name+".gtf", 'r') as f:
#this line opens the file in question
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
transcript_number = 0
for entry in f:
#this loop reads all lines in the source file one by one
Gen_finder = re.compile("gene_name")
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):
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"
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
transcript_number += 1
#the transcript number is updated (starting at on given that t
#he default is 0)
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")
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):
"""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:
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)
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,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__":
extract_transkript()
#This line allows the file to be executed on its own also from
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment