From ed61eddf2b014b9ad81ede62658b63c55196fe42 Mon Sep 17 00:00:00 2001
From: NMarthe <nina.marthe@ird.fr>
Date: Tue, 5 Dec 2023 13:05:49 +0100
Subject: [PATCH] fixed the output form
---
inference.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/inference.py b/inference.py
index 7a21b7d..f7c29a8 100644
--- a/inference.py
+++ b/inference.py
@@ -319,7 +319,7 @@ for cds_id in cds_var.keys():
# while printing the effect of the first snp we aso use the second one.
else: # size diff !=3k
- print("frameshift variation")
+ print("variation causing a frameshift")
old_frameshift=frame_shift
frame_shift=(frame_shift+length_ref-length_alt)%3
#Â frameshift=0 -> reading frame recovered. may need to get a base before.
@@ -342,8 +342,8 @@ for cds_id in cds_var.keys():
len_fragment_after_ins=(3-(len_fragment_before_ins+length_alt))%3
total_ins=sequence_target[posVar[1]-len_fragment_before_ins:posVar[1]+length_alt+len_fragment_after_ins]
total_del=cds.sequence[posVar[0]-len_fragment_before_del:posVar[0]+length_ref+len_fragment_after_del]
- stop=print_variation_change(total_del,total_ins)
print("recovery of the original reading frame")
+ stop=print_variation_change(total_del,total_ins)
if stop:
break
@@ -379,6 +379,5 @@ for cds_id in cds_var.keys():
if stop:
break
-
-
- print("\n")
\ No newline at end of file
+ print("\n")
+
--
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