From 856bcd0d4bf4cbc00098ec855d21ef4e26ad1786 Mon Sep 17 00:00:00 2001
From: Jakob Rien <jakobj.rien@stud.unibas.ch>
Date: Thu, 8 Dec 2022 07:59:32 +0000
Subject: [PATCH] Replace exon_length_filter.py
---
scripts/exon_length_filter.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/scripts/exon_length_filter.py b/scripts/exon_length_filter.py
index 23806d8..f8b4621 100644
--- a/scripts/exon_length_filter.py
+++ b/scripts/exon_length_filter.py
@@ -1,6 +1,6 @@
#### Exon length filter #####
"""Exon length filter
-Version 1.1.0"""
+Version 2.0.0"""
### Called Packages ###
import re
import os
@@ -159,11 +159,11 @@ def _exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),dep
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.
+ """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 saving the csv 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"""
@@ -176,8 +176,8 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo
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")
+ return(representative_transcript)
if __name__ == "__main__":
--
GitLab