From 49f7a4afcfe5963d048b44e976b41b96c11f0696 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Mon, 9 Mar 2020 15:33:26 +0100
Subject: [PATCH] src/db_utils/frequency_scripts/config_freq.py: modification
of iupac_dic variable : it links for each 'degenerated' nucleotides (SWKMRY)
the nucleotides they can be
---
src/db_utils/frequency_scripts/config_freq.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/db_utils/frequency_scripts/config_freq.py b/src/db_utils/frequency_scripts/config_freq.py
index 4f70c3c4..c30fdf52 100644
--- a/src/db_utils/frequency_scripts/config_freq.py
+++ b/src/db_utils/frequency_scripts/config_freq.py
@@ -71,8 +71,8 @@ class Config_freq:
output = Config.results / 'frequency_table'
output_exon_file = output / 'exon_freq.txt'
output_gene_file = output / 'gene_freq.txt'
- iupac_dic = {"S": ["G", "C"], "W": ["A", "T"], "K": ["G", "T"],
- "M": ["A", "C"], "R": ["A", "G"], "Y": ["C", "T"]}
+ iupac_dic = {"S": "[GC]", "W": "[AT]", "K": "[GT]",
+ "M": "[AC]", "R": "[AG]", "Y": "[CT]"}
nt_list = compute_nt_list()
aa_list = list("RHKDESTNQCGPAVILMFYW")
codon_list = [nt for nt in nt_list if len(nt) == 3]
--
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