def test_00_mysql_con(self):
args = deepcopy(self.default_args)
# Connect with MYSQL config
ac = AnnCoordinates(**args)
self.assertIsNotNone(ac.mysql_con)
# Connect with MYSQL connection
args['mysql_config'] = None
args['mysql_con'] = self.MYSQL_CON
ac = AnnCoordinates(**args)
self.assertIsNotNone(ac.mysql_con)
def test_07_ann_special_cases(self):
args = deepcopy(self.default_args)
# intergenic at left most side
ac = AnnCoordinates(**args)
ac.query('chr2', 100)
gene_info = ac.gene_info
self.assertIsNone(gene_info['id'])
self.assertEqual(gene_info['name'], 'intergenic(-,FAM110C)')
self.assertEqual(gene_info['type'], 'intergenic')
self.assertEqual(gene_info['start'], 0)
self.assertEqual(gene_info['end'], 38813)
self.assertIsNone(gene_info['source'])
self.assertIsNone(gene_info['strand'])
self.assertEqual(gene_info['intergenic_nearest']['name'], 'FAM110C')
self.assertEqual(gene_info['intergenic_nearest']['distance'], -38713)
# intergenic at right most side
ac = AnnCoordinates(**args)
ac.query('chr2', 243199373 - 100)
gene_info = ac.gene_info
self.assertIsNone(gene_info['id'])
self.assertEqual(gene_info['name'], 'intergenic(LINC01881,-)')
self.assertEqual(gene_info['type'], 'intergenic')
self.assertEqual(gene_info['start'], 243176659)
self.assertEqual(gene_info['end'], 0)
self.assertIsNone(gene_info['source'])
self.assertIsNone(gene_info['strand'])
self.assertEqual(gene_info['intergenic_nearest']['name'], 'LINC01881')
self.assertEqual(gene_info['intergenic_nearest']['distance'], 22614)
def test_05_ann_intergenic_igh_gene(self):
args = deepcopy(self.default_args)
ac = AnnCoordinates(**args)
# intergenic(IGHJ6,IGHJ5)
ac.query('chr14:106329469')
self.assertEqual(len(ac.gene_hits), 1)
gene_hit = ac.gene_hits[0]
self.assertIsNone(gene_hit['id'])
self.assertEqual(gene_hit['name'], 'IGHJ6')
self.assertEqual(gene_hit['type'], 'intergenic_igh')
self.assertIsNone(gene_hit['source'])
self.assertEqual(gene_hit['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_strand'], '-')
def test_04_ann_intergenic_gene(self):
args = deepcopy(self.default_args)
ac = AnnCoordinates(**args)
# intergenic(TMEM99,KRT12)
ac.query('chr17:39013407')
self.assertEqual(len(ac.gene_hits), 1)
gene_hit = ac.gene_hits[0]
self.assertIsNone(gene_hit['id'])
self.assertEqual(gene_hit['name'], 'intergenic(TMEM99,KRT12)')
self.assertEqual(gene_hit['type'], 'intergenic')
self.assertIsNone(gene_hit['source'])
self.assertIsNone(gene_hit['strand'])
self.assertEqual(gene_hit['intergenic_nearest']['name'], 'KRT12')
self.assertEqual(gene_hit['intergenic_nearest']['distance'], -4147)
def test_05_ann_intergenic_igh_gene(self):
args = deepcopy(self.default_args)
ac = AnnCoordinates(**args)
# IGHJ6 chr14:106329405-106329470
ac.query('chr14:106329469')
self.assertEqual(len(ac.gene_hits), 1)
gene_hit = ac.gene_hits[0]
# self.assertIsNone(gene_hit['id'])
self.assertEqual(gene_hit['name'], 'IGHJ6')
self.assertEqual(gene_hit['type'], 'protein_coding')
# self.assertIsNone(gene_hit['source'])
self.assertEqual(gene_hit['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_strand'], '-')
# IGHJ3P chr14:106329624-106329675
# intergenic(IGHJ6,IGHJ3P)
ac.query('chr14:106329500')
self.assertEqual(len(ac.gene_hits), 1)
gene_hit = ac.gene_hits[0]
self.assertIsNone(gene_hit['id'])
self.assertEqual(gene_hit['name'], 'IGHJ6')
self.assertEqual(gene_hit['type'], 'intergenic_igh')
self.assertIsNone(gene_hit['source'])
self.assertEqual(gene_hit['strand'], '-')
self.assertEqual(gene_hit['intergenic_nearest']['name'], 'IGHJ6')
self.assertEqual(gene_hit['intergenic_nearest']['distance'], 30)
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_strand'], '-')
def test_06_ann_beyond_transcript_range(self):
args = deepcopy(self.default_args)
# BCL6 without specifying transcript map
ac = AnnCoordinates(**args)
ac.query('chr3', 187462599)
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'BCL6')
self.assertEqual(gene_info['name'], 'BCL6')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['source'], 'RefSeq')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'NM_001706.5')
self.assertEqual(rank_info['trans_start'], 187439168)
self.assertEqual(rank_info['trans_end'], 187463256)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 10)
self.assertEqual(rank_info['cds_min'], 3)
self.assertEqual(rank_info['cds_max'], 10)
self.assertEqual(rank_info['rank'], "Intron1")
self.assertEqual(rank_info['exon_num'], 1)
# BCL6 with specifying transcript map
args['transcript_map'] = {
'NM_001130845'
}
ac = AnnCoordinates(**args)
ac.query('chr3', 187462599)
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'BCL6')
self.assertEqual(gene_info['name'], 'BCL6')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['source'], 'RefSeq')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'NM_001130845.2')
self.assertEqual(rank_info['trans_start'], 187439168)
self.assertEqual(rank_info['trans_end'], 187454289)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 10)
self.assertEqual(rank_info['cds_min'], 3)
self.assertEqual(rank_info['cds_max'], 10)
self.assertEqual(rank_info['rank'], "intragenic")
self.assertEqual(rank_info['exon_num'], -5)
def test_06_ann_beyond_transcript_range(self):
args = deepcopy(self.default_args)
# BCL6 without specifying transcript map
ac = AnnCoordinates(**args)
ac.query('chr3', 187462599)
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'ENSG00000113916.17')
self.assertEqual(gene_info['name'], 'BCL6')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['source'], 'HAVANA')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'ENST00000406870.6')
self.assertEqual(rank_info['trans_start'], 187439165)
self.assertEqual(rank_info['trans_end'], 187463515)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 10)
self.assertEqual(rank_info['cds_min'], 3)
self.assertEqual(rank_info['cds_max'], 10)
self.assertEqual(rank_info['rank'], "Intron1")
self.assertEqual(rank_info['exon_num'], 1)
# BCL6 with specifying transcript map
args['transcript_map'] = {
'ENST00000232014': {'gene': 'BCL6', 'refseq': 'NM_001130845'}
}
ac = AnnCoordinates(**args)
ac.query('chr3', 187462599)
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'ENSG00000113916.17')
self.assertEqual(gene_info['name'], 'BCL6')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['source'], 'HAVANA')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'ENST00000232014.8')
self.assertEqual(rank_info['trans_start'], 187440186)
self.assertEqual(rank_info['trans_end'], 187454357)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 10)
self.assertEqual(rank_info['cds_min'], 3)
self.assertEqual(rank_info['cds_max'], 10)
self.assertEqual(rank_info['rank'], "intragenic")
self.assertEqual(rank_info['exon_num'], -5)
def _test_ann_alk_(self, args):
"""
ALK Gene Structure
Chromosome: chr2
Genbank ID: NM_004304 Orientation: -
Length coding sequence : 4860 nucleotides.
Region start end region length phase at end
UTR 30,143,526 30,144,477
Exon 30,142,859 30,143,525 667 1
Exon 29,940,444 29,940,563 120 1
Exon 29,917,716 29,917,880 165 1
Exon 29,754,781 29,754,982 202 2
Exon 29,606,598 29,606,725 128 1
Exon 29,551,216 29,551,347 132 1
Exon 29,543,617 29,543,748 132 1
Exon 29,541,170 29,541,270 101 0
Exon 29,519,754 29,519,923 170 2
Exon 29,498,268 29,498,362 95 1
Exon 29,497,965 29,498,093 129 1
Exon 29,473,971 29,474,133 163 2
Exon 29,462,546 29,462,696 151 0
Exon 29,456,431 29,456,562 132 0
Exon 29,455,170 29,455,314 145 1
Exon 29,451,750 29,451,932 183 1
Exon 29,450,440 29,450,538 99 1
Exon 29,449,788 29,449,940 153 1
Exon 29,448,327 29,448,431 105 1
Exon 29,446,208 29,446,394 187 2
Exon 29,445,383 29,445,473 91 0
Exon 29,445,210 29,445,274 65 2
Exon 29,443,572 29,443,701 130 0
Exon 29,436,850 29,436,947 98 2
Exon 29,432,652 29,432,744 93 2
Exon 29,430,037 29,430,138 102 2
Exon 29,420,408 29,420,542 135 2
Exon 29,419,636 29,419,726 91 0
Exon 29,416,090 29,416,788 699 0
UTR 29,415,640 29,416,089
"""
# ALK chr2:29,415,640-30,144,477(GRCh37/hg19) from GeneCards
# ALK chr2:29,415,640-30,144,432(GRCh37/hg19) from GENCODE/HAVANA
# ENST00000389048 -> NM_004304
# Case01: Normal
ac = AnnCoordinates(**args)
# 5'UTR
ac.query('2:30,143,526')
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'ENSG00000171094.17')
self.assertEqual(gene_info['name'], 'ALK')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'ENST00000389048.7')
self.assertEqual(rank_info['trans_start'], 29415640)
self.assertEqual(rank_info['trans_end'], 30144432)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 29)
self.assertEqual(rank_info['cds_min'], 1)
self.assertEqual(rank_info['cds_max'], 29)
self.assertEqual(rank_info['rank'], "5'UTR")
self.assertEqual(rank_info['exon_num'], 1)
# Exon20
bp = np.random.choice(range(29446208, 29446394 + 1))
ac.query("2:{}".format(bp))
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'ENSG00000171094.17')
self.assertEqual(gene_info['name'], 'ALK')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'ENST00000389048.7')
self.assertEqual(rank_info['trans_start'], 29415640)
self.assertEqual(rank_info['trans_end'], 30144432)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 29)
self.assertEqual(rank_info['cds_min'], 1)
self.assertEqual(rank_info['cds_max'], 29)
self.assertEqual(rank_info['rank'], "Exon20")
self.assertEqual(rank_info['exon_num'], 20)
# Intron10
bp = np.random.choice(range(29498093 + 1, 29498268))
ac.query("2:{}".format(bp))
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'ENSG00000171094.17')
self.assertEqual(gene_info['name'], 'ALK')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'ENST00000389048.7')
self.assertEqual(rank_info['trans_start'], 29415640)
self.assertEqual(rank_info['trans_end'], 30144432)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 29)
self.assertEqual(rank_info['cds_min'], 1)
self.assertEqual(rank_info['cds_max'], 29)
self.assertEqual(rank_info['rank'], "Intron10")
self.assertEqual(rank_info['exon_num'], 10)
# 3'UTR
ac.query('2:29,415,640')
gene_info = ac.gene_info
self.assertEqual(gene_info['id'], 'ENSG00000171094.17')
self.assertEqual(gene_info['name'], 'ALK')
self.assertEqual(gene_info['type'], 'protein_coding')
self.assertEqual(gene_info['strand'], '-')
rank_info = ac.rank_info
self.assertEqual(rank_info['trans_id'], 'ENST00000389048.7')
self.assertEqual(rank_info['trans_start'], 29415640)
self.assertEqual(rank_info['trans_end'], 30144432)
self.assertEqual(rank_info['trans_strand'], '-')
self.assertEqual(rank_info['exon_total'], 29)
self.assertEqual(rank_info['cds_min'], 1)
self.assertEqual(rank_info['cds_max'], 29)
self.assertEqual(rank_info['rank'], "3'UTR")
self.assertEqual(rank_info['exon_num'], 29)
def test_03_ann_bp_handling(self):
args = deepcopy(self.default_args)
ac = AnnCoordinates(**args)
ac.query('2:30,143,526')
self.assertEqual(ac.chr_raw, '2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('2:30143526')
self.assertEqual(ac.chr_raw, '2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('chr2:30,143,526')
self.assertEqual(ac.chr_raw, 'chr2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('chr2:30143526')
self.assertEqual(ac.chr_raw, 'chr2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('2', '30,143,526')
self.assertEqual(ac.chr_raw, '2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('2', '30143526')
self.assertEqual(ac.chr_raw, '2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('2', 30143526)
self.assertEqual(ac.chr_raw, '2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('chr2', '30,143,526')
self.assertEqual(ac.chr_raw, 'chr2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('chr2', '30143526')
self.assertEqual(ac.chr_raw, 'chr2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)
ac.query('chr2', 30143526)
self.assertEqual(ac.chr_raw, 'chr2')
self.assertEqual(ac.chr, 'chr2')
self.assertEqual(ac.pos, 30143526)