Got rid of the class.

barcode/__init__.py

@@ -7,7 +7,7 @@ Copyright (c) 2013-2016 Jeroen F.J. Laros <J.F.J.Laros@lumc.nl>
 
 Licensed under the MIT license, see the LICENSE file.
 """
-from .barcode import BarCode
+from .barcode import filter_distance, all_barcodes, filter_stretches
 
 
 __version_info__ = ('0', '6', '0')

barcode/barcode.py

 import Levenshtein
 
 
-class BarCode(object):
-    """
-    Design and test NGS barcodes.
-    """
-    _nucleotides = ['A', 'C', 'G', 'T']
+_nucleotides = ['A', 'C', 'G', 'T']
 
-    def __init__(self, distance=Levenshtein.distance):
-        """
-        Initialise the class.
 
-        :arg function distance: Distance function.
-        """
-        self.distance = distance
-
-    def _all_words(self, bucket, word, length, result):
+def _all_words(bucket, word, length, result):
     """
     Generate all possible words of a certain length over a specified
     alphabet.
@@ -27,11 +16,12 @@ class BarCode(object):
     """
     if length:
         for i in bucket:
-                self._all_words(bucket, word + i, length - 1, result)
+            _all_words(bucket, word + i, length - 1, result)
     else:
         result.append(word)
 
-    def _filter_stretch(self, barcode, stretches):
+
+def _filter_stretch(barcode, stretches):
     """
     Test whether {barcode} contains none of the stretches in {stretches}.
 
@@ -46,7 +36,8 @@ class BarCode(object):
 
     return True
 
-    def _filter_distance(self, barcodes, candidate, min_dist):
+
+def _filter_distance(barcodes, candidate, min_dist, distance):
     """
     Test whether {candidate} can be added to {barcodes} based on the
     minimum distance between {candidate} and all barcodes in {barcodes}.
@@ -54,16 +45,18 @@ class BarCode(object):
     :arg list barcodes: List of barcodes.
     :arg str candidate: Candidate barcode.
     :arg int min_dist: Minimum distance between the barcodes.
+    :arg function distance: Distance function.
 
     :returns bool: True if the barcode is clean, False otherwise.
     """
     for i in barcodes:
-            if self.distance(i, candidate) < min_dist:
+        if distance(i, candidate) < min_dist:
             return False
 
     return True
 
-    def all_barcodes(self, length):
+
+def all_barcodes(length):
     """
     Generate all possible barcodes of a certain length.
 
@@ -73,11 +66,12 @@ class BarCode(object):
     """
     result = []
 
-        self._all_words(self._nucleotides, '', length, result)
+    _all_words(_nucleotides, '', length, result)
 
     return result
 
-    def filter_stretches(self, barcodes, max_stretch):
+
+def filter_stretches(barcodes, max_stretch):
     """
     Filter a list of barcodes for mononucleotide stretches.
 
@@ -86,21 +80,23 @@ class BarCode(object):
 
     :returns list: List of barcodes filtered for mononucleotide stretches.
     """
-        stretches = map(lambda x: (max_stretch + 1) * x, self._nucleotides)
+    stretches = map(lambda x: (max_stretch + 1) * x, _nucleotides)
     result = []
 
     for i in barcodes:
-            if self._filter_stretch(i, stretches):
+        if _filter_stretch(i, stretches):
             result.append(i)
 
     return result
 
-    def filter_distance(self, barcodes, min_dist):
+
+def filter_distance(barcodes, min_dist, distance=Levenshtein.distance):
     """
     Filter a list of barcodes for distance to other barcodes.
 
     :arg list barcodes: List of barcodes.
     :arg int min_dist: Minimum distance between the barcodes.
+    :arg function distance: Distance function.
 
     :returns list: List of barcodes filtered for distance to other
         barcodes.
@@ -108,7 +104,7 @@ class BarCode(object):
     result = []
 
     for i in barcodes:
-            if self._filter_distance(result, i, min_dist):
+        if _filter_distance(result, i, min_dist, distance):
             result.append(i)
 
     return result

barcode/cli.py

@@ -5,8 +5,8 @@ import sys
 
 import Levenshtein
 
-from . import doc_split, version, usage
-from .barcode import BarCode
+from . import doc_split, usage, version
+from .barcode import all_barcodes, filter_distance, filter_stretches
 
 
 def make_barcodes(length, max_stretch, min_dist, distance):
@@ -19,10 +19,8 @@ def make_barcodes(length, max_stretch, min_dist, distance):
     :arg int min_dist: Minimum distance between the barcodes.
     :arg function distance: Distance function.
     """
-    bc = BarCode(distance)
-
-    return bc.filter_distance(
-        bc.filter_stretches(bc.all_barcodes(length), max_stretch), min_dist)
+    return filter_distance(
+        filter_stretches(all_barcodes(length), max_stretch), min_dist)
 
 
 def test_barcodes(barcodes, min_dist, distance, handle):
@@ -32,12 +30,11 @@ def test_barcodes(barcodes, min_dist, distance, handle):
     :arg list barcodes: List of barcodes.
     :arg int min_dist: Minimum distance between the barcodes.
     :arg function distance: Distance function.
+    :arg steam handle: Open readable handle to a file.
 
     :returns int: The number of barcodes that violate the distance constraint.
     """
-    bc = BarCode(distance)
-
-    good_subset = bc.filter_distance(barcodes, min_dist)
+    good_subset = filter_distance(barcodes, min_dist)
     if handle:
         handle.write('\n'.join(good_subset))