src/nt_composition/config.py : Creation of a get_feature function to recover...

src/nt_composition/config.py : Creation of a get_feature function to recover the feature of interest

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