Update of the challenge class API

read_edges => edges
read_fasta => fasta

This functions are related to the build() not to the read() method.

Author: elmar-hinz

challenges/challenge.py

@@ -3,9 +3,10 @@
 This module holds the base class of all challenges.
 """
 
+import math
 import re
+
 import types
-import math
 
 
 class Challenge:
@@ -82,6 +83,10 @@ class Challenge:
     """
 
     fasta_pattern = '^[\-\*A-Z]+$'
+    """Reg expression for FASTA sequences.
+
+    Matches lines holding FASTA sequences.
+    """
 
     def __init__(self):
         self.lines = []
@@ -201,7 +206,7 @@ def line_to_edge(self, nr):
         match = re.compile(self.edge_pattern).match(self.line(nr))
         return self._to_edge(match)
 
-    def read_edges(self, start=0, stop=None):
+    def edges(self, start=0, stop=None):
         """Generator to read edges from lines.
 
         Reads a range of lines, one edge per line, and yields the edges.
@@ -229,7 +234,7 @@ def read_edges(self, start=0, stop=None):
             else:
                 break  # If edges end before stop, which may be infinity
 
-    def read_fasta(self, start=0, stop=None):
+    def fasta(self, start=0, stop=None):
         """Generator to read FASTA formatted samples.
 
         Reads multiple fasta sequences and yields them.

challenges/scaffold.py

@@ -75,6 +75,7 @@ def setUp(self):
     def test__init__(self):
         self.assertIsInstance(self.challenge, {}Challenge)
         self.assertIn('XXX', self.challenge.sample)
+        self.assertIn('XXX', self.challenge.expect)
 
     def test_build(self):
         self.skipTest('Not implemented.')

tests/test_challenge.py

@@ -1,4 +1,5 @@
 import unittest
+
 from types import SimpleNamespace
 
 from challenges import Challenge
@@ -102,8 +103,8 @@ def test_read_edges_from_to(self):
         5
         '''
         self.challenge.read()
-        result = self.challenge.read_edges(start=2, stop=4)
-        self.assertEqual(result.__name__, 'read_edges')
+        result = self.challenge.edges(start=2, stop=4)
+        self.assertEqual(result.__name__, 'edges')
         self.assertEqual(len(list(result)), 2)
 
     def test_read_edges_from(self):
@@ -117,7 +118,7 @@ def test_read_edges_from(self):
         5
         '''
         self.challenge.read()
-        result = self.challenge.read_edges(start=2)
+        result = self.challenge.edges(start=2)
         self.assertEqual(len(list(result)), 3)
 
     def test_read_edges_without_given_range(self):
@@ -128,7 +129,7 @@ def test_read_edges_without_given_range(self):
         3->9
         '''
         self.challenge.read()
-        result = self.challenge.read_edges()
+        result = self.challenge.edges()
         self.assertEqual(len(list(result)), 3)
 
     def test_read_fasta_from_to(self):
@@ -151,8 +152,8 @@ def test_read_fasta_from_to(self):
         14
         '''
         self.challenge.read()
-        result = self.challenge.read_fasta(start=5, stop=11)
-        self.assertEqual(result.__name__, 'read_fasta')
+        result = self.challenge.fasta(start=5, stop=11)
+        self.assertEqual(result.__name__, 'fasta')
         self.assertEqual(len(list(result)), 2)
 
     def test_read_fasta_from(self):
@@ -175,8 +176,8 @@ def test_read_fasta_from(self):
         14
         '''
         self.challenge.read()
-        result = self.challenge.read_fasta(start=5)
-        self.assertEqual(result.__name__, 'read_fasta')
+        result = self.challenge.fasta(start=5)
+        self.assertEqual(result.__name__, 'fasta')
         fasta = dict(result)
         self.assertEqual('AAATTT', fasta['FAS_4'])
         self.assertEqual(len(fasta), 3)
@@ -198,8 +199,8 @@ def test_read_fasta_without_given_range(self):
         TGGGAACCTGCGGGCAGTAGGTGGAAT
         '''
         self.challenge.read()
-        result = self.challenge.read_fasta()
-        self.assertEqual(result.__name__, 'read_fasta')
+        result = self.challenge.fasta()
+        self.assertEqual(result.__name__, 'fasta')
         self.assertEqual(len(list(result)), 4)
 
     def test_read_fasta_format(self):
@@ -218,8 +219,8 @@ def test_read_fasta_format(self):
         8
         '''
         self.challenge.read()
-        result = self.challenge.read_fasta(start=2)
-        self.assertEqual(result.__name__, 'read_fasta')
+        result = self.challenge.fasta(start=2)
+        self.assertEqual(result.__name__, 'fasta')
         fasta = dict(result)
         self.assertIn('FAS_1', fasta.keys())
         self.assertEqual('LLL---MMM*', fasta['FAS_1'])