diff --git a/scripts/Exon_length_filter.py b/scripts/exon_length_filter.py
similarity index 85%
rename from scripts/Exon_length_filter.py
rename to scripts/exon_length_filter.py
index 42979a9d67d376b6f70b2be30b25a1bf39ef00e3..4ccc8a94b78aa811796c8a6bdc3eeae8be3d0364 100644
--- a/scripts/Exon_length_filter.py
+++ b/scripts/exon_length_filter.py
@@ -3,8 +3,9 @@
### Called Packages ###
import re
import os
+import time
-import transkript_extractor as te
+import transcript_extractor as te
### Functions ###
def exon_length_calculator(entry):
@@ -52,10 +53,17 @@ def __longest_transcript_finder(current_exon_length,longest_transcript,longest_t
current_exon_length = 0
return(current_exon_length,longest_transcript,longest_transcript_ID)
+
+
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"""
- print("Representative trascripts are filterd based on exon length please wait...")
+ """This funtion selects only the transcripts for a dictionar that have the longest total mRNA"""
+
+ print("Representative trascipts are filterd 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)
+ gens_done = 0
+
with open(source_pathway_name+"\\"+file_name+".gtf", 'r') as f:
old_gen = str()
@@ -65,6 +73,7 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
longest_transcript_ID = str()
current_exon_length = 0
longest_transcript = 0
+ percentage_done = 0
for entry in f:
@@ -73,13 +82,14 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
except:
corrent_gen = old_gen
#The block above test if there is a gen name in the entry
- if corrent_gen != old_gen:
+ if corrent_gen != old_gen:
representative_trasnscript_not_found = True
+
#The block above determines if the Gen name is new and set the test
#representative_trasnscript_not_found back to true which is used to
#make the program faster if there is just one transcript for a given
#gen in the dict
- if representative_trasnscript_not_found and corrent_gen in gen_dict:
+ if representative_trasnscript_not_found and corrent_gen != str():
#print(corrent_gen)
#The conditon prvents serges if a representative transcript has
#all ready been chosen
@@ -88,7 +98,14 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
representative_transcript[old_gen] = longest_transcript_ID
try:
del gen_dict[old_gen]
- old_gen = corrent_gen
+ old_gen = corrent_gen
+ gens_done += 1
+ corrent_percentage_done = (gens_done/total_genes)*100
+ if corrent_percentage_done > percentage_done+10:
+ bar,start_time = te.bar_builder(percentage=percentage_done+10,length_multiplyer = 3,start_time=start_time,bar =bar)
+ percentage_done = int(corrent_percentage_done)
+
+
except:
old_gen = corrent_gen
longest_transcript = 0
@@ -107,7 +124,7 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
continue
try:
- current_transcript_ID = te.transcript_ID_finder(entry)
+ current_transcript_ID = te.transcript_ID_finder(entry)
except:
continue
#The block above searches for a trnascript ID in the current enty
@@ -132,10 +149,11 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
current_exon_length,longest_transcript,longest_transcript_ID = __longest_transcript_finder(current_exon_length,longest_transcript,longest_transcript_ID,old_transcript_ID)
representative_transcript[old_gen] = longest_transcript_ID
del representative_transcript[str()]
- print("Representative transcripts collected\n")
+ te.bar_builder(100,length_multiplyer = 3,start_time=start_time,bar =bar)
return(representative_transcript)
if __name__ == "__main__":
exon_length_filter()
-#This line allows the file to be executed on its own also from
\ No newline at end of file
+
+#This line allows the file to be executed on its own also from
diff --git a/scripts/transkript_extractor.py b/scripts/trancript_extractor.py
similarity index 97%
rename from scripts/transkript_extractor.py
rename to scripts/trancript_extractor.py
index 9f69a0dfd1f44c667aef63e65458234cd83d1996..054b92f9d6bf1d88c83de8888c704aab4c4af8de 100644
--- a/scripts/transkript_extractor.py
+++ b/scripts/trancript_extractor.py
@@ -12,7 +12,7 @@ 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+"_intermediat_file.txt"
+ Search_profile = file_name+"_intermediate_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>")
@@ -163,7 +163,7 @@ def _transcript_extractor (file_name,source_pathway_name,deposit_pathway_name):
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")
+ 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