refactor code at parsers

Author: FilomenoSanchez

parsers/casprr2parser.py

@@ -1,5 +1,4 @@
-from operator import itemgetter
-from utils import unique_by_key
+from utils import get_unique_distances
 from utils.exceptions import InvalidFormat
 
 
@@ -34,8 +33,5 @@ def CASPRR2Parser(input, input_format=None):
     if not output:
         raise InvalidFormat('Unable to parse CASPRR_MODE_2 file')
     else:
-        unique_contacts = unique_by_key(output, key=itemgetter(0))
-        output = [(*contact[0], *contact[1:]) for contact in unique_contacts]
-        output = sorted(output, key=itemgetter(2), reverse=True)
-        output.append('DISTO')
-        return output
+        unique_contacts = get_unique_distances(output)
+        return unique_contacts

parsers/ccmpredparser.py

@@ -1,6 +1,5 @@
-from operator import itemgetter
 from utils.exceptions import InvalidFormat
-from utils import unique_by_key
+from utils import get_unique_contacts
 
 
 def CCMpredParser(input, input_format=None):
@@ -31,7 +30,5 @@ def CCMpredParser(input, input_format=None):
     if not output:
         raise InvalidFormat('Unable to parse contacts')
     else:
-        unique_contacts = unique_by_key(output, key=itemgetter(0))
-        output = [(*contact[0], contact[1]) for contact in unique_contacts]
-        output = sorted(output, key=itemgetter(2), reverse=True)
-        return output
+        unique_contacts = get_unique_contacts(output)
+        return unique_contacts

parsers/contactparser.py

@@ -1,7 +1,6 @@
 from enum import Enum
-from operator import itemgetter
 import re
-from utils import unique_by_key
+from utils import get_unique_contacts
 from utils.exceptions import InvalidFormat
 
 
@@ -138,7 +137,5 @@ def ContactParser(input, input_format):
     if not output:
         raise InvalidFormat('Unable to parse contacts')
     else:
-        unique_contacts = unique_by_key(output, key=itemgetter(0))
-        output = [(*contact[0], contact[1]) for contact in unique_contacts]
-        output = sorted(output, key=itemgetter(2), reverse=True)
-        return output
+        unique_contacts = get_unique_contacts(output)
+        return unique_contacts

parsers/npzparser.py

@@ -1,9 +1,8 @@
 import io
 import base64
 import numpy as np
-from operator import itemgetter
 from utils.exceptions import InvalidFormat
-from utils import unique_by_key
+from utils import get_unique_distances
 
 
 def parse_array(array):
@@ -31,7 +30,6 @@ def NpzParser(input, input_format=None):
     except (OSError, KeyError, IndexError) as e:
         raise InvalidFormat('Unable to parse distance NPZ file')
 
-
     for contact in tmp_output:
         # contact = [res_1, res_2, raw_score, distance_bin, distance_score]
         contact[:2] = sorted(contact[:2], reverse=True)
@@ -40,8 +38,5 @@ def NpzParser(input, input_format=None):
     if not output:
         raise InvalidFormat('Unable to parse NPZ file')
     else:
-        unique_contacts = unique_by_key(output, key=itemgetter(0))
-        output = [(*contact[0], *contact[1:]) for contact in unique_contacts]
-        output = sorted(output, key=itemgetter(2), reverse=True)
-        output.append('DISTO')
-        return output
+        unique_contacts = get_unique_distances(output)
+        return unique_contacts

utils/__init__.py

@@ -1,4 +1,5 @@
 import os
+from operator import itemgetter
 from enum import Enum
 
 
@@ -110,6 +111,7 @@ class UrlIndex(Enum):
     YOUTUBE_EMBED = 'https://www.youtube.com/embed/dQw4w9WgXcQ'
     YOUTUBE_LINK = 'https://www.youtube.com/watch?v=dQw4w9WgXcQ'
 
+
 def create_ConPlot(*args, **kwargs):
     from utils.plot_utils import create_ConPlot
 
@@ -236,9 +238,19 @@ def get_session_action(*args, **kwargs):
     return get_session_action(*args, **kwargs)
 
 
-def unique_by_key(elements, key=None):
+def get_unique_contacts(elements):
     # Credits to: https://stackoverflow.com/questions/31499259/making-a-sequence-of-tuples-unique-by-a-specific-element
-    if key is None:
-        # no key: the whole element must be unique
-        key = lambda e: e
-    return list({key(el): el for el in elements}.values())
+    key = itemgetter(0)
+    unique = list({key(el): el for el in elements}.values())
+    output = [(*contact[0], contact[1]) for contact in unique]
+    output = sorted(output, key=itemgetter(2), reverse=True)
+    return output
+
+
+def get_unique_distances(elements):
+    key = itemgetter(0)
+    unique_contacts = list({key(el): el for el in elements}.values())
+    output = [(*contact[0], *contact[1:]) for contact in unique_contacts]
+    output = sorted(output, key=itemgetter(2), reverse=True)
+    output.append('DISTO')
+    return output