From 9f5e877412776879036f6ab947a24ad522710249 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Mon, 9 Mar 2020 15:34:12 +0100
Subject: [PATCH] src/db_utils/frequency_scripts/frequency_function.py:
modification of frequencies for better performances
---
.../frequency_scripts/frequency_function.py | 28 ++++++++-----------
1 file changed, 11 insertions(+), 17 deletions(-)
diff --git a/src/db_utils/frequency_scripts/frequency_function.py b/src/db_utils/frequency_scripts/frequency_function.py
index 4e8c0cac..19bc7a2e 100644
--- a/src/db_utils/frequency_scripts/frequency_function.py
+++ b/src/db_utils/frequency_scripts/frequency_function.py
@@ -12,6 +12,7 @@ from typing import Iterable, Dict, List
import logging
from Bio.Seq import Seq
import numpy as np
+import regex as re
def frequencies(sequence: str, nt_list: Iterable[str]) -> Dict[str, float]:
@@ -24,23 +25,16 @@ def frequencies(sequence: str, nt_list: Iterable[str]) -> Dict[str, float]:
"""
if not full_defined(sequence) or len(sequence) < 3:
return {nt: np.nan for nt in nt_list}
- dic = {nt: 0. for nt in nt_list}
seql = len(sequence)
- for i, n in enumerate(sequence):
- for nt in nt_list:
- ntl = len(nt)
- if ntl == 1:
- if nt in ["S", "W", "K", "M", "R", "Y"]:
- if n in Config_freq.iupac_dic[nt]:
- dic[nt] += 1 / seql * 100
- else:
- if n == nt:
- dic[nt] += 1 / seql * 100
- else:
- if sequence[i:i + ntl] == nt:
- dic[nt] += 1 / (seql - ntl + 1) * 100
- for nt in nt_list:
- dic[nt] = round(dic[nt], 5)
+ dic = {}
+ for n in nt_list:
+ if n in Config_freq.iupac_dic.keys():
+ pat = re.compile(Config_freq.iupac_dic[n])
+ else:
+ pat = re.compile(n)
+ seqlen = seql - len(n) + 1
+ dic[n] = round((len(list(re.findall(pat, sequence, overlapped=True)))
+ / seqlen) * 100, 5)
return dic
@@ -57,7 +51,7 @@ def compute_dic(dic_seq: Dict[str, Seq], coord: List[str],
sequence = dic_seq[coord[0]][int(coord[1]): int(coord[2])]
if coord[3] == "-":
sequence = sequence.reverse_complement()
- return frequencies(sequence, nt_list)
+ return frequencies(str(sequence), nt_list)
def get_ft_type(ft: str) -> str:
--
GitLab