From 4c635b507af5ca7c0fe5180e1a195d65b8de6c3d Mon Sep 17 00:00:00 2001
From: NMarthe <nina.marthe@ird.fr>
Date: Tue, 5 Dec 2023 15:36:23 +0100
Subject: [PATCH] deleted functions not used
---
Functions.py | 92 ----------------------------------------------------
1 file changed, 92 deletions(-)
diff --git a/Functions.py b/Functions.py
index 18386a2..57ee334 100644
--- a/Functions.py
+++ b/Functions.py
@@ -485,95 +485,3 @@ def invert_segment_list(seg_list):
list_inverted.append(inv_seg)
return list(reversed(list_inverted))
-
-
-
-# pour faire l'inférence, lire le fichier variations.txt et l'interpréter. pour chaque variation, regarder ce que ça fait.
-# donc première étape quand on appelle la fct "inférence", c'est d'ajouter dans les features leur séquence avec seg_seq et la liste des segments.
-
-def add_feature_sequence(feature,seg_seq):
- feature_sequence=""
- for segment in feature.segments_list:
- if segment==feature.segments_list[0]:
- feature_sequence+=get_segment_sequence(seg_seq,segment)[feature.pos_start-1:] # revérifier les +/- 1 pour la position, avec de vraies données
- elif segment==feature.segments_list[-1]:
- feature_sequence+=get_segment_sequence(seg_seq,segment)[0:feature.pos_stop] # revérifier les +/- 1 pour la position, avec de vraies données
- else:
- feature_sequence+=get_segment_sequence(seg_seq,segment)
- feature.sequence=feature_sequence
-
-def transcription(dna_sequence):
- rna_sequence=""
- for dna_base in dna_sequence:
- match dna_base:
- case "A":
- rna_sequence+="U"
- case "C":
- rna_sequence+="G"
- case "G":
- rna_sequence+="C"
- case "T":
- rna_sequence+="A"
- return rna_sequence
-
-# penser à transcrire la séquence codante du gène !!
-def get_aa(codon):
- match codon[0:2]:
- case "UU":
- if (codon[2]=="U") | (codon[2]=="C"):
- return "Phe"
- else:
- return "Leu"
- case "UC":
- return "Ser"
- case "UA":
- if (codon[2]=="U") | (codon[2]=="C"):
- return "Tyr"
- else:
- return "Stop"
- case "UG":
- if (codon[2]=="U") | (codon[2]=="C"):
- return "Cys"
- elif codon[2]=="A":
- return "Stop"
- else:
- return "Trp"
- case "CU":
- return "Leu"
- case "CC":
- return "Pro"
- case "CA":
- if (codon[2]=="U") | (codon[2]=="C"):
- return "His"
- else:
- return "Gln"
- case "CG":
- return "Arg"
- case "AU":
- if codon[2]=="G":
- return "Met"
- else:
- return "Ile"
- case "AC":
- return "Thr"
- case "AA":
- if (codon[2]=="U") | (codon[2]=="C"):
- return "Asn"
- else:
- return "Lys"
- case "AG":
- if (codon[2]=="U") | (codon[2]=="C"):
- return "Ser"
- else:
- return "Arg"
- case "GU":
- return "Val"
- case "GC":
- return "Ala"
- case "GA":
- if (codon[2]=="U") | (codon[2]=="C"):
- return "Asp"
- else:
- return "Glu"
- case "GG":
- return "Gly"
\ No newline at end of file
--
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