def test_total_file_in_block(self):
embl_file = os.path.join(data_dir, 'annotation.embl')
blocks = [Block(1, 600, 600, 10, 'x')]
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(4, len(genes))
self.assertEqual('knockout', genes[0].category())
def test_fully_contained_three(self):
embl_file = os.path.join(data_dir, 'annotation.embl')
blocks = [Block(1, 200, 110, 10, 'x')]
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(3, len(genes))
self.assertEqual('knockout', genes[0].category())
def test_downregulated_neg(self):
embl_file = os.path.join(data_dir, 'annotation.embl')
blocks = [Block(90, 110, 20, -10, 'decreased_insertions')]
blocks[0].direction = 'reverse'
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(
"1_100 decreased_mutants_at_end_of_gene 0 100 -10.0 decreased_insertions reverse NA",
str(genes[0]))
def test_block_near_end_reverse(self):
embl_file = os.path.join(data_dir, 'reverse.embl')
blocks = [Block(1, 20, 20, 10, 'x')]
blocks[0].direction = 'forward'
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(1, len(genes))
self.assertEqual('increased_mutants_at_end_of_gene',
genes[0].category())
def test_block_near_end_decrease(self):
embl_file = os.path.join(data_dir, 'annotation.embl')
blocks = [Block(90, 110, 20, -10, 'x')]
blocks[0].direction = 'reverse'
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(1, len(genes))
self.assertEqual('decreased_mutants_at_end_of_gene',
genes[0].category())
self.assertEqual('1_100', genes[0].gene_name)
def test_fabI(self):
blocks = [Block(1345296, 1345494, (1345494 - 1345296), 10, 'xx')]
blocks[0].direction = 'reverse'
embl_file = os.path.join(data_dir, 'prime.embl')
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(1, len(genes))
self.assertEqual(
'fabI upregulated 1344507 1345296 10 xx reverse yciW__3prime',
str(genes[0]))
def test_increased_knockout(self):
embl_file = os.path.join(data_dir, 'prime.embl')
blocks = [
Block(3984512, 3987059, (3987059 - 3984512), 10,
'increased_insertions')
]
blocks[0].direction = 'forward'
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(
"cyaA knockout 3984512 3987059 10 increased_insertions forward yifL",
str(genes[0]))
def gene_statistics(self, forward_plotfile, reverse_plotfile,
combined_plotfile, window_size):
b = BlockIdentifier(combined_plotfile, forward_plotfile,
reverse_plotfile, window_size)
blocks = b.block_generator()
annotationfile = self.emblfile
if self.use_annotation:
annotationfile = self.annotation_file
genes = GeneAnnotator(self.annotation_file, blocks).annotate_genes()
intergenic_blocks = [block for block in blocks if block.intergenic]
print("#Genes: ", len(genes))
print("#Integenic Blocks: ", len(intergenic_blocks))
# Consolidate all similar adjacent windows if annotation is not used
if not self.use_annotation:
all_genes = self.merge_windows(genes)
else: # merge 3'prime and 5'prime windows
gene_3primes = []
gene_5primes = []
all_genes = []
for g in genes:
if "__3prime" in g.gene_name:
gene_3primes.append(g)
elif "__5prime" in g.gene_name:
gene_5primes.append(g)
else:
all_genes.append(g)
merged_3primes = self.merge_windows(gene_3primes)
merged_5primes = self.merge_windows(gene_5primes)
for mw in merged_3primes:
all_genes.append(mw)
for mw in merged_5primes:
all_genes.append(mw)
if len(all_genes) == 0 and len(intergenic_blocks) == 0:
return []
self.write_gene_report(all_genes, intergenic_blocks)
self.write_regulated_gene_report(all_genes, intergenic_blocks)
#if self.verbose:
#self.print_genes_intergenic(genes,intergenic_blocks)
return all_genes
def test_real_annotation_prime(self):
blocks = [
Block(2804038, 2804236, (2804236 - 2804038), 10,
'decreased_insertions'),
Block(2804128, 2804659, (2804659 - 2804128), 10,
'decreased_insertions'),
Block(2804587, 2804785, (2804785 - 2804587), 10,
'decreased_insertions'),
Block(3309373, 3309571, (3309571 - 3309373), -10,
'increased_insertions'),
Block(3309397, 3310885, (3310885 - 3309397), -10,
'increased_insertions'),
Block(3309199, 3309397, (3309397 - 3309199), 10,
'increased_insertions'),
Block(3310714, 3310912, (3310912 - 3310714), 10,
'increased_insertions'),
Block(3339819, 3340017, (3340017 - 3339819), 10,
'increased_insertions'),
Block(3339936, 3340428, (3340428 - 3339936), -10,
'decreased_insertions'),
Block(3340428, 3340626, (3340626 - 3340428), -10,
'decreased_insertions'),
Block(3340473, 3341328, (3341328 - 3340473), -10,
'decreased_insertions'),
Block(3340275, 3340473, (3340473 - 3340275), -10,
'decreased_insertions'),
Block(3341126, 3341324, (3341324 - 3341126), -10,
'decreased_insertions'),
Block(3423124, 3423382, (3423382 - 3423124), -10,
'decreased_insertions'),
Block(3423382, 3423580, (3423580 - 3423382), -10,
'decreased_insertions'),
Block(3423378, 3424197, (3424197 - 3423378), -10,
'decreased_insertions'),
Block(3424003, 3424201, (3424201 - 3424003), -10,
'decreased_insertions'),
Block(3429855, 3430053, (3430053 - 3429855), -10,
'decreased_insertions'),
Block(3429876, 3431253, (3431253 - 3429876), -10,
'decreased_insertions'),
Block(3431184, 3431382, (3431382 - 3431184), -10,
'decreased_insertions'),
Block(3510665, 3510863, (3510863 - 3510665), 10,
'increased_insertions'),
Block(3510756, 3511845, (3511845 - 3510756), 10,
'increased_insertions'),
Block(3511703, 3511901, (3511901 - 3511703), 10,
'increased_insertions'),
Block(3516110, 3516308, (3516308 - 3516110), 10,
'increased_insertions'),
Block(3516229, 3518782, (3518782 - 3516229), 10,
'increased_insertions'),
Block(3599810, 3602009, (3602009 - 3599810), 10,
'increased_insertions'),
Block(3602009, 3602207, (3602207 - 3602009), 10,
'increased_insertions'),
Block(3602110, 3602356, (3602356 - 3602110), 10,
'increased_insertions'),
Block(3601912, 3602110, (3602110 - 3601912), -10,
'decreased_insertions'),
Block(3900952, 3901726, (3901726 - 3900952), -10,
'decreased_insertions'),
Block(3901726, 3901924, (3901924 - 3901726), -10,
'decreased_insertions'),
Block(3901746, 3901810, (3901810 - 3901746), -10,
'decreased_insertions'),
Block(3901548, 3901746, (3901746 - 3901548), 10,
'increased_insertions'),
Block(3901810, 3902008, (3902008 - 3901810), 10,
'increased_insertions'),
Block(3901908, 3902799, (3902799 - 3901908), 10,
'increased_insertions'),
Block(3901710, 3901908, (3901908 - 3901710), 10,
'increased_insertions'),
Block(3984512, 3987059, (3987059 - 3984512), 10,
'increased_insertions'),
Block(3986900, 3987098, (3987098 - 3986900), 10,
'increased_insertions'),
Block(3991259, 3991457, (3991457 - 3991259), 10,
'increased_insertions'),
Block(3991342, 3993505, (3993505 - 3991342), 10,
'increased_insertions'),
Block(3993311, 3993509, (3993509 - 3993311), 10,
'increased_insertions'),
Block(3993453, 3993651, (3993651 - 3993453), 10,
'increased_insertions'),
Block(4026466, 4026664, (4026664 - 4026466), 10,
'increased_insertions'),
Block(4026504, 4027956, (4027956 - 4026504), 10,
'increased_insertions'),
Block(4027769, 4027967, (4027967 - 4027769), 10,
'increased_insertions'),
Block(4391769, 4391967, (4391967 - 4391769), 10,
'increased_insertions'),
Block(4391854, 4393114, (4393114 - 4391854), 10,
'increased_insertions'),
Block(4392918, 4393116, (4393116 - 4392918), -10,
'decreased_insertions'),
Block(4530773, 4531376, (4531376 - 4530773), 10,
'decreased_insertions'),
Block(4531853, 4532450, (4532450 - 4531853), -10,
'decreased_insertions'),
Block(4533480, 4533678, (4533678 - 4533480), 10,
'decreased_insertions'),
Block(4533544, 4534084, (4534084 - 4533544), -10,
'decreased_insertions'),
Block(4534084, 4534282, (4534282 - 4534084), 10,
'increased_insertions'),
Block(4534120, 4534846, (4534846 - 4534120), -10,
'decreased_insertions'),
Block(4533922, 4534120, (4534120 - 4533922), 10,
'increased_insertions'),
Block(4534846, 4535044, (4535044 - 4534846), -10,
'increased_insertions'),
Block(4534912, 4537549, (4537549 - 4534912), 10,
'increased_insertions'),
Block(4534714, 4534912, (4534912 - 4534714), -10,
'increased_insertions'),
Block(4537360, 4537558, (4537558 - 4537360), 10,
'increased_insertions'),
Block(1345296, 1345494, (1345494 - 1345296), -10,
'increased_insertions')
]
blocks[0].direction = 'forward'
blocks[1].direction = 'forward'
blocks[2].direction = 'reverse'
blocks[3].direction = 'reverse'
blocks[4].direction = 'reverse'
blocks[5].direction = 'reverse'
blocks[6].direction = 'nodirection'
blocks[7].direction = 'nodirection'
blocks[8].direction = 'nodirection'
blocks[9].direction = 'nodirection'
blocks[10].direction = 'nodirection'
blocks[11].direction = 'nodirection'
blocks[12].direction = 'nodirection'
blocks[13].direction = 'nodirection'
blocks[14].direction = 'nodirection'
blocks[15].direction = 'nodirection'
blocks[16].direction = 'nodirection'
blocks[17].direction = 'nodirection'
blocks[18].direction = 'nodirection'
blocks[19].direction = 'forward'
blocks[20].direction = 'forward'
blocks[21].direction = 'forward'
blocks[22].direction = 'nodirection'
blocks[23].direction = 'nodirection'
blocks[24].direction = 'forward'
blocks[25].direction = 'forward'
blocks[26].direction = 'forward'
blocks[27].direction = 'forward'
blocks[28].direction = 'forward'
blocks[29].direction = 'forward'
blocks[30].direction = 'forward'
blocks[31].direction = 'forward'
blocks[32].direction = 'forward'
blocks[33].direction = 'forward'
blocks[34].direction = 'forward'
blocks[35].direction = 'forward'
blocks[36].direction = 'forward'
blocks[37].direction = 'forward'
blocks[38].direction = 'forward'
blocks[39].direction = 'forward'
blocks[40].direction = 'forward'
blocks[41].direction = 'nodirection'
blocks[42].direction = 'nodirection'
blocks[43].direction = 'nodirection'
blocks[44].direction = 'nodirection'
blocks[45].direction = 'nodirection'
blocks[46].direction = 'nodirection'
blocks[47].direction = 'nodirection'
blocks[48].direction = 'reverse'
blocks[49].direction = 'forward'
blocks[50].direction = 'forward'
blocks[51].direction = 'forward'
blocks[52].direction = 'nodirection'
blocks[53].direction = 'forward'
blocks[54].direction = 'nodirection'
blocks[55].direction = 'nodirection'
blocks[56].direction = 'nodirection'
blocks[57].direction = 'nodirection'
blocks[58].direction = 'reverse'
blocks[59].direction = 'reverse'
embl_file = os.path.join(data_dir, 'prime.embl')
a = GeneAnnotator(embl_file, blocks)
genes = a.annotate_genes()
self.assertEqual(41, len(genes))