From 69116bb5c91c1ebf009e80afe294ccda569c9e6a Mon Sep 17 00:00:00 2001
From: "nina.marthe_ird.fr" <nina.marthe@ird.fr>
Date: Mon, 19 Feb 2024 16:35:04 +0100
Subject: [PATCH] added function to get a chromosome's path
---
Functions.py | 27 ++++++++++++++++++---------
1 file changed, 18 insertions(+), 9 deletions(-)
diff --git a/Functions.py b/Functions.py
index d8c2717..68065c7 100644
--- a/Functions.py
+++ b/Functions.py
@@ -306,15 +306,24 @@ def compare_strand(list_1,list_2,list_1_unstrand,list_2_unstrand):
same_strand_count+=1
return [seg_common,same_strand_count]
-def add_target_genome_path(feature_id,target_genome_path):
- feature=Features[feature_id]
- list_seg=feature.segments_list_source
- first_seg=get_first_seg(list_seg)
- last_seg=get_first_seg(reversed(list_seg))
- feature_path=[]
- if first_seg!='':
- feature_path=get_feature_path(target_genome_path,first_seg,last_seg)
- feature.segments_list_target=feature_path
+def get_chr_path(feature_id,target_genome_paths):
+ feat_chr_number=Features[feature_id].chr[3:]
+ for path_name in target_genome_paths.keys():
+ if feat_chr_number in path_name[-3:]:
+ return target_genome_paths[path_name]
+ return False
+
+def add_target_genome_path(feature_id,target_genome_paths):
+ target_genome_path=get_chr_path(feature_id,target_genome_paths)
+ if target_genome_paths!=False:
+ feature=Features[feature_id]
+ list_seg=feature.segments_list_source
+ first_seg=get_first_seg(list_seg)
+ last_seg=get_first_seg(reversed(list_seg))
+ feature_path=[]
+ if first_seg!='':
+ feature_path=get_feature_path(target_genome_path,first_seg,last_seg)
+ feature.segments_list_target=feature_path
def get_feature_path(target_genome_path,first_seg,last_seg):
# find the path in target genome
--
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