def decreased_insertions_blocks(self, masking_plot): blocks = [] inblock = False start = 0 end = 0 max_logfc = 0 for i, mask in enumerate(masking_plot.combined): if mask < 0 and not inblock: inblock = True start = i max_logfc = mask elif mask < 0 and inblock: if max_logfc > mask: max_logfc = mask elif mask >= 0 and inblock: inblock = False end = i blocks.append(Block(start +1, end, end-start, max_logfc, 'decreased_insertions' )) max_logfc = 0 # Check for block at end if inblock: blocks.append(Block(start +1, len(masking_plot.combined), len(masking_plot.combined)-start, max_logfc, 'decreased_insertions')) return blocks
def blocks_create(self, logfc_values):
blocks = []
inblock = False
start = 0
end = 0
max_logfc = 0
abs_logfc_values = numpy.absolute(logfc_values)
for i in range(0, self.genome_length):
lfc = abs_logfc_values[i]
if lfc > 0 and not inblock:
inblock = True
start = i
max_logfc = logfc_values[i]
elif lfc > 0 and inblock:
if numpy.absolute(max_logfc) < lfc:
max_logfc = logfc_values[i]
elif lfc <= 0 and inblock:
inblock = False
end = i
blocks.append(
Block(start + 1, end, end - start, max_logfc, 'x'))
max_logfc = 0
# Check for block at end
if inblock:
blocks.append(
Block(start + 1, len(logfc_values),
len(logfc_values) - start, max_logfc, 'x'))
return blocks
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 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_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_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_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_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_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))