fasta as aminoacids

VoSeq · Aug 5, 2015 · e56c576 · e56c576
1 parent 29fc9da
commit e56c576
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Showing 3 changed files with 34 additions and 1 deletion.
diff --git a/voseq/create_dataset/dataset.py b/voseq/create_dataset/dataset.py
@@ -202,11 +202,20 @@ def convert_lists_to_dataset(self, partitions):
                 else:
                     line_contents = line.split('\n')
                     taxon = line_contents[0]
+                    voucher_code = taxon.replace('>', '').split('_')[0]
                     sequence = line_contents[1]
 
                     if self.aminoacids is not True and this_gene != '' and \
                             self.translations is True:
                         sequence = self.degenerate(sequence, this_gene)
+
+                    if self.aminoacids is True:
+                        sequence = self.translate_this_sequence(
+                            sequence,
+                            this_gene,
+                            voucher_code,
+                        )
+
                     out += '\n'
                     out += '\n'.join([taxon, sequence])
 

diff --git a/voseq/create_dataset/tests/tests_create_fasta_dataset.py b/voseq/create_dataset/tests/tests_create_fasta_dataset.py
@@ -110,3 +110,27 @@ def test_create_dataset_degenerated_warning_data_cannot_be_of_partial_codons(sel
                         )
         expected = 'Cannot degenerate codons if they you have not selected all codon positions'
         self.assertTrue(expected in str(c.content))
+
+    def test_fasta_as_aminoacids(self):
+        self.c.post('/accounts/login/', {'username': 'admin', 'password': 'pass'})
+        c = self.c.post('/create_dataset/results/',
+                        {
+                            'voucher_codes': 'CP100-10',
+                            'gene_codes': 3,  # wingless
+                            'geneset': '',
+                            'taxonset': '',
+                            'translations': True,
+                            'introns': 'YES',
+                            'file_format': 'FASTA',
+                            'degen_translations': 'NORMAL',
+                            'exclude': 'YES',
+                            'aminoacids': True,
+                            'special': False,
+                            'outgroup': '',
+                            'positions': 'ALL',
+                            'partition_by_positions': 'ONE',
+                            'taxon_names': ['CODE', 'GENUS', 'SPECIES'],
+                        }
+                        )
+        expected = 'GKSTTTGHLIYKCGGIDKRTIEKFEKEAQEM'
+        self.assertTrue(expected in str(c.content))
diff --git a/voseq/create_dataset/utils.py b/voseq/create_dataset/utils.py
@@ -86,7 +86,7 @@ def create_dataset(self):
             fasta = CreateFasta(self.codon_positions, self.partition_by_positions,
                                 self.seq_objs, self.gene_codes, self.voucher_codes,
                                 self.file_format, degen_translations=self.degen_translations,
-                                translations=self.translations)
+                                translations=self.translations, aminoacids=self.aminoacids)
             fasta_dataset = fasta.from_seq_objs_to_dataset()
             self.warnings += fasta.warnings
             self.dataset_file = fasta.dataset_file