1st, 2nd and 3rd codons, 1st2nd_3rd

VoSeq · Feb 15, 2015 · 75cb34b · 75cb34b
1 parent ec6e82a
commit 75cb34b
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diff --git a/voseq/create_dataset/tests/tests_utils.py b/voseq/create_dataset/tests/tests_utils.py
@@ -706,6 +706,32 @@ def test_dataset_1st_2nd_codons_1st2nd_3rd(self):
 ????????????????TGGCGGATATGGACTCCTAGCTATATCGACGATTGGAACCAGTTTTATGGGAGACAATTAAAACATGTACGCCAGCTTATATATTTTTATGTATCCATATATGGGGTTGGAATGCTGTCCTTATTTGGGCCCGAATGCTTCCCGATAATAATAGTTTGTTTTCCCCTCTTATCTTTATTCAGAGATGTGAAAGGGCGGACGGTGACGTTACCCCCTTCTCAAATGCCAAGGGGCTCGTGATTGCATTTTCTTCATTGCGGATTCTCATTTGGGCATAATTATACACATATAAATCGATAAAAATTCTAGACAATCCTTTTGTTGGCGTGGATACGCTTCTCTTTTTTCTTCCGTTTGCGGGCATACATCTTTACGACGAACTAAACTCTTTTGATCTGGGGGGGGACC??????????????????????
 >CP100-11_Melitaea_diamina
 ?TAGCGTAAATGTAATCCAATCTATATCAACGATAGAATCTATTTTAATGAGTGTCAATTTATACATGAAAGTCTGTTTATAAATTTTTAAGTAGCAATAAATGAGATTGTATTACTGACATAAATGGAGCCAGTAAGTTCCCCAAAATTTAAAATTTATATGCTCATCTAATCTTAATTAATAAATGAGAATGGGAGAATGATAAAGTTCCCCACTTATTATATGCCTAAGAGTTAGGGTTAGTATTTTTTACTTAGTGGATTCTTACTAGAGTATATTTATATAAATATATAACAATATATAATTTTGTCAAACTTATTGATAGAGAGAATAAGATACTCCTATATTTACAGTTAGTGAGTATATAACTTAAGGTCAATCTATACTATTTTGTTCTCGAGAGAGTC??????????????????????
+"""
+        result = dataset_creator.dataset_str
+        self.assertEqual(expected.strip(), result)
+
+    def test_dataset_1st_2nd_3rd_codons_1st2nd_3rd(self):
+        g1 = Genes.objects.get(gene_code='COI')
+        cleaned_data = self.cleaned_data
+        cleaned_data['gene_codes'] = [g1]
+        del cleaned_data['positions']
+        cleaned_data['positions'] = ['1st', '2nd', '3rd']
+        cleaned_data['partition_by_positions'] = '1st2nd_3rd'
+
+        dataset_creator = CreateDataset(cleaned_data)
+        expected = """
+>coi_1st_2nd_codons
+--------------------
+>CP100-10_Papilionoidea_Melitaea_diamina
+????????????????TGGCGGATATGGACTCCTAGCTATATCGACGATTGGAACCAGTTTTATGGGAGACAATTAAAACATGTACGCCAGCTTATATATTTTTATGTATCCATATATGGGGTTGGAATGCTGTCCTTATTTGGGCCCGAATGCTTCCCGATAATAATAGTTTGTTTTCCCCTCTTATCTTTATTCAGAGATGTGAAAGGGCGGACGGTGACGTTACCCCCTTCTCAAATGCCAAGGGGCTCGTGATTGCATTTTCTTCATTGCGGATTCTCATTTGGGCATAATTATACACATATAAATCGATAAAAATTCTAGACAATCCTTTTGTTGGCGTGGATACGCTTCTCTTTTTTCTTCCGTTTGCGGGCATACATCTTTACGACGAACTAAACTCTTTTGATCTGGGGGGGGACC??????????????????????
+>CP100-11_Melitaea_diamina
+?TAGCGTAAATGTAATCCAATCTATATCAACGATAGAATCTATTTTAATGAGTGTCAATTTATACATGAAAGTCTGTTTATAAATTTTTAAGTAGCAATAAATGAGATTGTATTACTGACATAAATGGAGCCAGTAAGTTCCCCAAAATTTAAAATTTATATGCTCATCTAATCTTAATTAATAAATGAGAATGGGAGAATGATAAAGTTCCCCACTTATTATATGCCTAAGAGTTAGGGTTAGTATTTTTTACTTAGTGGATTCTTACTAGAGTATATTTATATAAATATATAACAATATATAATTTTGTCAAACTTATTGATAGAGAGAATAAGATACTCCTATATTTACAGTTAGTGAGTATATAACTTAAGGTCAATCTATACTATTTTGTTCTCGAGAGAGTC??????????????????????
+>coi_3rd_codon
+--------------------
+>CP100-10_Papilionoidea_Melitaea_diamina
+????????ACTATTACATTTTACAAATTTTATATTATTTCTAATTTTTATTTATGATATAATTTATAAAAGACATATCCAATTAATAAGTACATTATATATAATGAATAAATCCATATTTCTAATAGTATTTTATATGTCTCAATTTTTTATTTAATTTATTTAATATAAAAATAAATCAATAATATATTTATAGTATTTCATTTCCAAAT???????????
+>CP100-11_Melitaea_diamina
+GCGTTGCCTGTTTGCATGACGTTTGAAATAACTTCCACTTTTTTTTTCTTTGGTGAGTTCTTTGCCATCTCGTAATGTGTTCCCTTTTTCGGTTAAGCGCGGCTACCTCCATCAGGCCTATCTTCTATCGTCCTTGCTATTCCTTATGTAATCAAATCTTTGCTGTCCTTTTTCTCTTCGCTCTTTCAGATACCTTACGGGGAC???????????
 """
         result = dataset_creator.dataset_str
         self.assertEqual(expected.strip(), result)
diff --git a/voseq/create_dataset/utils.py b/voseq/create_dataset/utils.py
@@ -551,6 +551,36 @@ def from_seq_objs_to_fasta(self):
             out += '\n'.join(partitions['codons1_2'])
             return out
 
+        if '1st' in self.codon_positions and '2nd' in self.codon_positions and \
+                '3rd' in self.codon_positions and \
+                '1st2nd_3rd' in self.partition_by_positions:
+            for gene_code in self.seq_objs:
+                this_gene = None
+                for seq_record in self.seq_objs[gene_code]:
+
+                    if this_gene is None:
+                        this_gene = seq_record.name
+
+                        seq_str = '>' + this_gene + '_1st_2nd_codons\n' + '--------------------'
+                        partitions['codons1_2'].append(seq_str)
+
+                        seq_str = '>' + this_gene + '_3rd_codon\n' + '--------------------'
+                        partitions['codon3'].append(seq_str)
+
+                    codons = self.get_sequence_based_on_codon_positions(this_gene, seq_record.seq)
+
+                    seq_str = '>' + seq_record.id + '\n' + str(chain_and_flatten(codons[0], codons[1]))
+                    partitions['codons1_2'].append(seq_str)
+
+                    seq_str = '>' + seq_record.id + '\n' + str(codons[2])
+                    partitions['codon3'].append(seq_str)
+
+            out = ''
+            out += '\n'.join(partitions['codons1_2'])
+            out += '\n'
+            out += '\n'.join(partitions['codon3'])
+            return out
+
     def get_taxon_names_for_taxa(self):
         """Returns dict: {'CP100-10': {'taxon': 'name'}}