From 8c23055a701e1d70419c4b079a4cb4598a5884a4 Mon Sep 17 00:00:00 2001
From: Jakob Rien <jakobj.rien@stud.unibas.ch>
Date: Tue, 13 Dec 2022 07:55:32 +0000
Subject: [PATCH] Replace exon_length_filter.py
Inputs have changed for the main function !!!!
---
scripts/exon_length_filter.py | 24 +++++++++++-------------
1 file changed, 11 insertions(+), 13 deletions(-)
diff --git a/scripts/exon_length_filter.py b/scripts/exon_length_filter.py
index f8b4621..4ee1fdd 100644
--- a/scripts/exon_length_filter.py
+++ b/scripts/exon_length_filter.py
@@ -1,11 +1,16 @@
#### Exon length filter #####
"""Exon length filter
-Version 2.0.0"""
+Version 2.1.0"""
### Called Packages ###
import re
import os
import transcript_extractor as te
+
+python_version = "3.7.13"
+module_list =[re,os]
+modul_name_list = ["re","os"]
+
### Functions ###
def exon_length_calculator(entry):
@@ -158,30 +163,23 @@ def _exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),dep
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):
+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 filters a dictionary of genes and there transcripts by the length of there exons an selects the longes transcript for each gene and returns an dictionary {gene_ID : transcript_ID}.
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 files
- 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"""
+ gen_dict:dict{key == gene ID:[transcript IDs that belong to that gene]}"""
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)
- print("\nRepresentative transcripts collected")
+ representative_transcript = _exon_length_filter(file_name,source_pathway_name,deposit_pathway_name,gen_dict)
+ print("\nRepresentative transcripts collected")
return(representative_transcript)
if __name__ == "__main__":
- help(exon_length_filter)
+ te.version_control(module_list,modul_name_list,python_version)
exon_length_filter()
--
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