From d193ff23ec977d7a105a097469e56609a3f7fd86 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 18 Jun 2020 09:58:30 +0200
Subject: [PATCH] src/nt_composition/config.py : Creation of a get_feature
function to recover the feature of interest
---
src/nt_composition/config.py | 42 ++++++++++++++++++++++++++++++++++--
1 file changed, 40 insertions(+), 2 deletions(-)
diff --git a/src/nt_composition/config.py b/src/nt_composition/config.py
index 504ca2ab..ae790526 100644
--- a/src/nt_composition/config.py
+++ b/src/nt_composition/config.py
@@ -8,6 +8,7 @@ file that will be produced by this module.
"""
from ..db_utils.config import Config
+from typing import List
def get_weight_folder(weight: int, global_weight: int):
@@ -68,6 +69,7 @@ def get_density_recap(weight: int, global_weight: int,
seen in `global_weight` project are taken into account
:param ft_type: A feature type
:param ft: A feature
+ :param fig: Say if the result file is a figure or not
:return:
"""
if fig:
@@ -88,7 +90,42 @@ def get_interaction_file(weight: int):
concider
:return: The interaction filename
"""
- return ConfigNt.interaction / f"interaction_number_weight>={weight}_by_project.txt"
+ return ConfigNt.interaction / \
+ f"interaction_number_weight>={weight}_by_project.txt"
+
+
+def get_features(ft_type: str) -> List[str]:
+ """
+ Get all the feature corresponding to `ft_type`.
+
+ :param ft_type: The feature type of interest
+ :return: The list of feature type of interest
+ """
+ nt_list = ["A", "C", "G", "T"]
+ if ft_type == 'nt':
+ return nt_list + ["S", "W"]
+ elif ft_type == 'dnt':
+ return [a + b for a in nt_list for b in nt_list]
+ elif ft_type == 'tnt' or ft_type == 'codon':
+ return [a + b + c for a in nt_list for b in nt_list for c in nt_list]
+ elif ft_type == 'aa':
+ return list("RHKDESTNQCGPAVILMFYW")
+ else:
+ return ['Hydrophobicity_Goldsack', 'Hydrophobicity_Sweet',
+ 'Hydrophobicity_Kyte_Doolittle', 'Hydrophobicity_Tanford',
+ 'accessible_resiudues_Janin', 'burried_resiudues_Rose',
+ 'Disorder_promoting_Campen',
+ 'Disorder_propensity_Russel_Linding',
+ 'Disorder_propensity_Deleage_Roux',
+ 'intrinsically_unstructured_proteins_Tompa',
+ 'Interface_propensity_Jones', 'Linker_propensity_Bae',
+ 'Flexibility_Vihinen', 'Stability_Zhou_Zhou',
+ 'Bulkiness_Zimmerman', 'Molecular_weight_Fasman',
+ 'Molecular_weight_Dawson', 'Polarity_Radzicka',
+ 'Isoelectric_Point_Zimmerman', 'Alpha-helix_Deleage',
+ 'Beta-sheet_Deleage', 'Coil_conformation_Deleage',
+ 'Positive_charge_Fauchere', 'Negative_charge_Fauchere',
+ 'Sequence_freq_Jungck']
class ConfigNt:
@@ -105,4 +142,5 @@ class ConfigNt:
density_folder = output_folder / 'density_fig'
get_density_recap = get_density_recap
selected_project = interaction / "selected_sample.txt"
- get_density_file = get_density_file
\ No newline at end of file
+ get_density_file = get_density_file
+ get_features = get_features
--
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