def test_simple_get_lbp_list(self): cls = self.__class__ cds_simple = sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 1, 3, 55) self.assertEqual(cds_simple.get_lbp_list(), cls.loc_list_short_1) cds_simple = sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 2, 59, 165) self.assertEqual(cds_simple.get_lbp_list(), cls.loc_list_short_2)
def test_simple_str(self): cls = self.__class__ test_gene_seq = sequencing.GeneSequence("SYMB1", "teamcx", cls.short_gff, 1, "Bmin.gene1", 0, 56) mRNA_simple = sequencing.mRNAGene("SYMB1", "teamcx", cls.short_gff, 1, 1, 2) cds_simple = sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 1, 3, 55) line_list = [ ">Features Bmin.gene1", "5616\t26521\tgene", "\t\t\tlocus_tag\tSYMB1_0001", ] line_list.append(str(mRNA_simple)) line_list.append(str(cds_simple)) expected = '\n'.join(line_list) self.assertEqual(str(test_gene_seq), expected) # Test the second gene test_gene_seq = sequencing.GeneSequence("SYMB1", "teamcx", cls.short_gff, 2, "Bmin.gene2", 56, 165) mRNA_simple = sequencing.mRNAGene("SYMB1", "teamcx", cls.short_gff, 2, 57, 58) cds_simple = sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 2, 59, 165) line_list = [ ">Features Bmin.gene2", "53720\t81789\tgene", "\t\t\tlocus_tag\tSYMB1_0002", ] line_list.append(str(mRNA_simple)) line_list.append(str(cds_simple)) expected = '\n'.join(line_list) self.assertEqual(str(test_gene_seq), expected)
def test_1_gene_str(self): cls = self.__class__ test_gene_seq = sequencing.GeneSequence("SYMB1", "teamcx", cls.gff_1, 1, "Bmin.gene1", 0, 55) mRNA_simple = sequencing.mRNAGene("SYMB1", "teamcx", cls.short_gff, 1, 1, 2) cds_simple = sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 1, 3, 55) line_list = [ ">Features Bmin.gene1", "5616\t26521\tgene", "\t\t\tlocus_tag\tSYMB1_0001", ] line_list.append(str(mRNA_simple)) line_list.append(str(cds_simple)) expected = '\n'.join(line_list) self.assertEqual(str(test_gene_seq), expected)
def test_simple_str(self): cls = self.__class__ cds_simple = sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 1, 3, 55) first_line = "26430\t26521\tCDS" intermediary_locs = '\n'.join( map(lambda tup_: "{}\t{}".format(tup_[0], tup_[1]), cls.loc_list_short_1[1:])) protein_info = "\t\t\tproduct PROTEIN_ANNOTATION\n" + \ "\t\t\tprotein_id gnl|teamcx|SYMB1_0001\n" + \ "\t\t\ttranscript_id gnl|teamcx|mrna.SYMB1_0001" expected = first_line + '\n' + intermediary_locs + '\n' + protein_info self.assertEqual(str(cds_simple), expected) # Test the second gene cds_simple = sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 2, 59, 165) first_line = "81761\t81789\tCDS" intermediary_locs = '\n'.join( map(lambda tup_: "{}\t{}".format(tup_[0], tup_[1]), cls.loc_list_short_2[1:])) protein_info = "\t\t\tproduct PROTEIN_ANNOTATION\n" + \ "\t\t\tprotein_id gnl|teamcx|SYMB1_0002\n" + \ "\t\t\ttranscript_id gnl|teamcx|mrna.SYMB1_0002" expected = first_line + '\n' + intermediary_locs + '\n' + protein_info self.assertEqual(str(cds_simple), expected)
def test_construction(self): cls = self.__class__ sequencing.CDSGene("SYMB1", "teamcx", cls.short_gff, 1, 3, 55)