default values for outgroup is None

VoSeq · Mar 16, 2015 · f205b4d · f205b4d
1 parent 8129955
commit f205b4d
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Showing 5 changed files with 8 additions and 3 deletions.
diff --git a/voseq/create_dataset/dataset.py b/voseq/create_dataset/dataset.py
@@ -9,7 +9,7 @@ class Dataset(object):
     Base class to create datasets from Seq objects into FASTA, TNT formats.
     """
     def __init__(self, codon_positions, partition_by_positions, seq_objs, gene_codes,
-                 voucher_codes, file_format, outgroup, voucher_codes_metadata):
+                 voucher_codes, file_format, outgroup=None, voucher_codes_metadata=None):
         self.outgroup = outgroup
         self.file_format = file_format
         self.codon_positions = codon_positions

diff --git a/voseq/create_dataset/tests/tests_create_tnt_dataset.py b/voseq/create_dataset/tests/tests_create_tnt_dataset.py
@@ -28,6 +28,7 @@ def setUp(self):
             'positions': ['2nd', '3rd'],
             'partition_by_positions': 'ONE',
             'file_format': 'TNT',
+            'outgroup': '',
         }
 
         self.c = Client()

diff --git a/voseq/create_dataset/tests/tests_utils.py b/voseq/create_dataset/tests/tests_utils.py
@@ -28,6 +28,7 @@ def setUp(self):
             'positions': ['ALL'],
             'partition_by_positions': 'ONE',
             'file_format': 'FASTA',
+            'outgroup': '',
         }
 
         self.c = Client()

diff --git a/voseq/create_dataset/tests/tests_views.py b/voseq/create_dataset/tests/tests_views.py
@@ -19,6 +19,7 @@ def setUp(self):
             'taxonset': None,
             'voucher_codes': 'CP100-10\r\nCP100-11',
             'geneset': None,
+            'outgroup': '',
         }
 
         self.c = Client()
@@ -43,8 +44,8 @@ def test_view_result(self):
                               'degen_translations': 'NORMAL',
                               'exclude': 'YES',
                               'aminoacids': False,
-                              'outgroup': '',
                               'special': False,
+                              'outgroup': '',
                           }
                           )
         self.assertEqual(200, res.status_code)

diff --git a/voseq/create_dataset/utils.py b/voseq/create_dataset/utils.py
@@ -155,7 +155,9 @@ def create_dataset(self):
         self.create_seq_objs()
 
         if self.file_format == 'FASTA':
-            fasta = CreateFasta(self.codon_positions, self.partition_by_positions, self.seq_objs, self.gene_codes, self.voucher_codes, self.file_format)
+            fasta = CreateFasta(self.codon_positions, self.partition_by_positions,
+                                self.seq_objs, self.gene_codes, self.voucher_codes,
+                                self.file_format)
             fasta_dataset = fasta.from_seq_objs_to_dataset()
             self.warnings += fasta.warnings
             return fasta_dataset