diff --git a/scripts/Excecution_file.py b/scripts/Excecution_file.py
new file mode 100644
index 0000000000000000000000000000000000000000..788525eb4438f485ed1e2a554be3f61ccc102170
--- /dev/null
+++ b/scripts/Excecution_file.py
@@ -0,0 +1,20 @@
+### Imports ###
+import os
+
+import transkript_extractor as te
+import Exon_length_filter as elf
+import representative_v4 as rtcl
+
+### Scipt ###
+def exe(file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name = os.getcwd(),Input_free = True):
+ file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transkript(file_name,source_pathway_name,deposit_pathway_name,Input_free = Input_free)
+ inter_mediate_file_directory = os.path.join(deposit_pathway_name,file_name+"_intermediate_file.txt")
+ print("Transcripts are filterd based on transcipt score please wait...")
+ pre_filter_representative_transcripts_dict = rtcl.find_repr_by_SupportLevel(inter_mediate_file_directory)
+ print("Transcripts filtered\n")
+ elf.exon_length_filter(file_name,source_pathway_name,deposit_pathway_name,gen_dict= pre_filter_representative_transcripts_dict,Input_free = Input_free)
+ return(file_name,source_pathway_name,deposit_pathway_name)
+### from consol ####
+##D:\\Uni\\Sem 9\\Programing in the Life sciences\\Projekt\\Intermediat Files
+if __name__ == "__main__":
+ exe()
\ No newline at end of file
diff --git a/scripts/exon_length_filter.py b/scripts/Exon_length_filter.py
similarity index 63%
rename from scripts/exon_length_filter.py
rename to scripts/Exon_length_filter.py
index 2ebfb4f0f00feaa9b3810b3a914b3959a9fc6bc2..162ff1f302b4ef144d9c34bde47b5b69c4ba72c0 100644
--- a/scripts/exon_length_filter.py
+++ b/scripts/Exon_length_filter.py
@@ -1,57 +1,76 @@
#### Exon length filter #####
-
+"""Exon length filter
+Version 1.1.0"""
### Called Packages ###
import re
import os
-import transcript_extractor as te
+import transkript_extractor as te
### Functions ###
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",""))
- final_index_start_coordinates = entry.find(try_find_start_coordinates[0])+len(try_find_start_coordinates[0])-1
+ #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",""))
- exon_length = end_coordinates-start_coordinates
+ #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
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)
+ exon_lenght = "NA"
+ return(exon_lenght)
def exon_fider(entry):
- """This funtion determines if a given entry belongs to an exon"""
+ """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 function encapsulates an operation that has to be carried out multiple times in the exon_length_filter"""
+ """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"""
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 function selects only the transcripts that have the longest total mRNA"""
-
- print("Representative transcipts are filtered based on exon length. Please wait...")
+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"""
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)
gens_done = 0
- with open(source_pathway_name+"\\"+file_name+".gtf", 'r') as f:
+ with open(os.path.join(source_pathway_name,file_name+".gtf"), 'r') as f:
old_gen = str()
old_transcript_ID = str()
@@ -114,7 +133,7 @@ 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 transcript ID in the current enty
+ #The block above searches for a trnascript ID in the current enty
if current_transcript_ID in transcript_IDs:
#This condition test if the Transcript is one of the
@@ -139,6 +158,31 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
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"]},Input_free = False):
+ """This function filters a dictionary of genes and there transcripts by the length of there exons an selects the longes transcript for each gene ans saves tham in a "," seperated csv file.
+ 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 saving the csv file
+ gen_dict:dict{key == gene ID:[transcript IDs that belong to that gene]}
+ Input_free: tuple ; default = False # this input should be set to True for automation"""
+
+ 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)
+ if Input_free:
+ pre_existing_file = False
+ else:
+ search_profile = file_name+"_"+"representative_transcripts"+".csv"
+ pre_existing_file = te.__searche_for_preexisting_files(search_profile,deposit_pathway_name)
+ if pre_existing_file == False:
+ representative_transcript = _exon_length_filter(file_name,source_pathway_name,deposit_pathway_name,gen_dict)
+ _representative_transcript_csv(representative_transcript,file_name,deposit_pathway_name)
+ print("\nRepresentative transcripts collected")
+
+
if __name__ == "__main__":
+ help(exon_length_filter)
exon_length_filter()
+
+#This line allows the file to be executed on its own also from
\ No newline at end of file
diff --git a/scripts/transcript_extractor.py b/scripts/transkript_extractor.py
similarity index 75%
rename from scripts/transcript_extractor.py
rename to scripts/transkript_extractor.py
index 1b901a70677f4049b6cc1eca325e0bd6d354470a..6bcd13bd151ae173cfbacfd57ebb2a247320c669 100644
--- a/scripts/transcript_extractor.py
+++ b/scripts/transkript_extractor.py
@@ -1,5 +1,6 @@
#### Transcript extractor #####
-
+"""Transcript extractor
+Version 1.1.0"""
### Called Packages ###
import re
import os
@@ -68,10 +69,9 @@ def __searche_for_preexisting_files(file_name,deposit_pathway_name = os.getcwd()
generat_new_file = False
directory_content = os.listdir(deposit_pathway_name)
for file in directory_content:
- Search_profile = file_name+"_intermediate_file.txt"
- if file == Search_profile:
+ if file == file_name:
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>")
+ 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
@@ -88,10 +88,17 @@ def __searche_for_preexisting_files(file_name,deposit_pathway_name = os.getcwd()
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")
+ 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)))
@@ -164,7 +171,9 @@ 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 find the gene ID of a known gene 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:]
@@ -173,7 +182,9 @@ def gene_ID_finder(entry):
return (gene_ID)
def transcript_ID_finder (entry):
- """This function is supposed to finde the transcript ID in a known transcript 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:]
@@ -186,7 +197,9 @@ def transcript_ID_finder (entry):
return (transcript_ID)
def transcript_support_level_finder(entry):
- """This function is supposed to find the transcript support level in a known transcript 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:]
@@ -210,10 +223,15 @@ def transcript_support_level_finder(entry):
def _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name):
- """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:
+ """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(source_pathway_name+"\\"+file_name+".gtf", 'r') as f:
+ 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)
@@ -221,7 +239,7 @@ def _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name):
Old_gen_ID = str()
#stand-in as the first couple entrys are not genes
- with open(deposit_pathway_name+"\\"+file_name+"_"+"intermediate_file"+".txt","w") as IMF:
+ with open(os.path.join(deposit_pathway_name,file_name+"_"+"intermediate_file"+".txt"),"w") as IMF:
transcript_number = 0
for entry in f:
@@ -255,20 +273,33 @@ def _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name):
print("The transcripts have been collected")
-def extract_transkript (file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name = True):
+def extract_transkript (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.
- 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 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)
- 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)
+ 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 ####