Fixed seeds in certain methods to provide deterministic background co…

…mpositon and stable results.
dmitrymyl · Oct 22, 2021 · bd9b48a · bd9b48a
1 parent 5ee5a3e
commit bd9b48a
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Showing 4 changed files with 20 additions and 13 deletions.
diff --git a/ortho2align/cli_scripts.py b/ortho2align/cli_scripts.py
@@ -38,7 +38,7 @@
 bg_from_inter_ranges_processing_group.add_argument('-seed',
                                                    type=int,
                                                    nargs='?',
-                                                   default=123,
+                                                   default=0,
                                                    help='random seed number for sampling intergenic regions (default: %(default)s).')
 bg_from_inter_ranges_output_group = bg_from_inter_ranges_parser.add_argument_group('Output')
 bg_from_inter_ranges_output_group.add_argument('-output',
@@ -82,7 +82,7 @@
 bg_from_shuffled_ranges_processing_group.add_argument('-seed',
                                                       type=int,
                                                       nargs='?',
-                                                      default=123,
+                                                      default=0,
                                                       help='random seed number for sampling intergenic regions (default: %(default)s).')
 bg_from_shuffled_ranges_output_group = bg_from_shuffled_ranges_parser.add_argument_group('Output')
 bg_from_shuffled_ranges_output_group.add_argument('-output',
@@ -161,7 +161,7 @@
 estimate_background_processing_group.add_argument('-seed',
                                                   type=int,
                                                   nargs='?',
-                                                  default=123,
+                                                  default=0,
                                                   help='random seed for sampling scores (default: %(default)s).')
 estimate_background_processing_group.add_argument('--silent',
                                                   action='store_true',

diff --git a/ortho2align/genomicranges.py b/ortho2align/genomicranges.py
@@ -1762,14 +1762,16 @@ def inter_ranges(self, distance=0, verbose=False):
 
     def shuffle_inside_chrom(self, seed=0):
         shuffled_granges = []
+        local_random = random.Random()
+        local_random.seed(seed)
         for grange in self:
             chromsize = self.sequence_file.chromsizes.get(grange.chrom)
             if chromsize is None:
                 end = grange.end
             else:
                 end = chromsize.size - len(grange)
             try:
-                shuffled_start = random.randint(0, end)
+                shuffled_start = local_random.randint(0, end)
             except ValueError:
                 shuffled_start = 0
             shuffled_end = shuffled_start + len(grange)
@@ -1786,7 +1788,9 @@ def shuffle_inside_chrom(self, seed=0):
     def sample_granges(self, n, seed=0):
         if n > len(self):
             raise ValueError(f'Value of n={n} is greater than number of genomic ranges: {len(self)}.')
-        sample = random.sample(self, n)
+        local_random = random.Random()
+        local_random.seed(seed)
+        sample = local_random.sample(self, n)
         used_args = {'collection', }
         kwargs = {attr: getattr(self, attr)
                   for attr in set(self.init_args) - used_args}

diff --git a/ortho2align/pipeline.py b/ortho2align/pipeline.py
@@ -84,7 +84,8 @@ def bg_from_inter_ranges(genes_filename,
         seed (int): a random seed (default: 0).
         silent (bool): if True, will suppress a progress bar (default: False).
     """
-    random.seed(seed)
+    local_random = random.Random()
+    local_random.seed(seed)
 
     cmd_hints = ['parsing the annotation...',
                  'sampling intergenic regions...',
@@ -103,8 +104,8 @@ def bg_from_inter_ranges(genes_filename,
         if len(inter_genes) < sample_size:
             raise ValueError(f'The number of observations ({sample_size}) '
                              'must be less than the number of intergenic '
-                             f'regions ({len(inter_genes)}) derived from genes')
-        samples = BaseGenomicRangesList(random.sample(inter_genes, k=sample_size))
+                             f'regions ({len(inter_genes)}) derived from genes.')
+        samples = BaseGenomicRangesList(local_random.sample(inter_genes, k=sample_size))
 
         pbar.update()
 
@@ -226,8 +227,9 @@ def _estimate_bg_for_single_query_blast(query, bg_ranges, word_size, output_name
             scores += alignment_scores
         score_size = len(scores)
         if score_size > observations:
-            random.seed(seed)
-            scores = random.sample(scores, observations)
+            local_random = random.Random()
+            local_random.seed(seed)
+            scores = local_random.sample(scores, observations)
         with open(output_name, 'w') as outfile:
             json.dump(scores, outfile)
         return output_name, score_size
@@ -264,8 +266,9 @@ def _estimate_bg_for_single_query_seqfile(query, seqfile, word_size, output_name
         scores = [hsp.score for hsp in alignment.HSPs]
         score_size = len(scores)
         if score_size > observations:
-            random.seed(seed)
-            scores = random.sample(scores, observations)
+            local_random = random.Random()
+            local_random.seed(seed)
+            scores = local_random.sample(scores, observations)
         with open(output_name, 'w') as outfile:
             json.dump(scores, outfile)
         return score_size

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 
 setup(name='ortho2align',
-      version='0.9',
+      version='1.0.1',
       description='A lncRNA ortholog discovery tool based on syntenic regions and statistical assessment of alignment nonrandomness.',
       url='http://github.com/dmitrymyl/ortho2align',
       author='Dmitry Mylarshchikov',