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)