def make_predictions_csv_response(predictions, args):
up = args.get_upstream()
down = args.get_downstream()
size = up + down + 1
if args.is_custom_ranges_list():
size = None
separator = ','
if args.get_format() == 'tsv':
separator = '\t'
headers = ['Name', 'ID', 'Max', 'Chromosome', 'Start', 'End']
if args.is_custom_ranges_list():
headers = ['Chromosome', 'Start', 'End', 'Max']
if args.get_include_all():
if args.is_custom_ranges_list():
headers.append('Values')
else:
headers.extend([str(i) for i in range(-1*up, down+1)])
yield separator.join(headers) + '\n'
for prediction in predictions:
items = []
if args.is_custom_ranges_list():
items = [prediction['chrom'], str(prediction['start']), str(prediction['end']), str(prediction['max'])]
else:
start = prediction['start']
end = prediction['end']
items = [
prediction['commonName'],
prediction['name'],
str(prediction['max']),
prediction['chrom'],
str(start),
str(end)]
if args.get_include_all():
items.extend(get_all_values(prediction, size))
yield separator.join(items) + '\n'
def test_get_all_values_without_size(self):
prediction = {
'start': 0,
'end': 5,
'values': [{
'start': 1,
'value': 1.2
}]
}
expected = ['0', '1.2', '0', '0', '0']
self.assertEqual(expected, get_all_values(prediction, None))
def test_negative_values_guess_with_size(self):
prediction = {
'start': 0,
'end': 5,
'values': [{
'start': 1,
'value': -1.2
}]
}
expected = ['0', '-1.2', '0', '0', '0', '0']
self.assertEqual(expected, get_all_values(prediction, 6))
def make_download_custom_result(separator, include_all, predictions):
headers = ['Name', 'Sequence', 'Max']
if include_all:
headers.append('Values')
yield separator.join(headers) + '\n'
for prediction in predictions:
items = [
prediction['name'],
prediction['sequence'],
str(prediction['max'])
]
if include_all:
items.extend(get_all_values(prediction, len(prediction['sequence'])))
yield separator.join(items) + '\n'
def make_download_custom_result(separator, include_all, predictions):
headers = ['Name', 'Sequence', 'Max']
if include_all:
headers.append('Values')
yield separator.join(headers) + '\n'
for prediction in predictions:
items = [
prediction['name'], prediction['sequence'],
str(prediction['max'])
]
if include_all:
items.extend(
get_all_values(prediction, len(prediction['sequence'])))
yield separator.join(items) + '\n'
def test_overlap_most_extreem_value_wins(self):
prediction = {
'start': 0,
'end': 5,
'values': [
{
'start': 1,
'value': 1.2
},
{
'start': 1,
'value': -1.3
},
]
}
expected = ['0', '-1.3', '0', '0', '0']
self.assertEqual(expected, get_all_values(prediction, None))
def make_predictions_csv_response(predictions, args):
up = args.get_upstream()
down = args.get_downstream()
size = up + down + 1
if args.is_custom_ranges_list():
size = None
separator = ','
if args.get_format() == 'tsv':
separator = '\t'
headers = ['Name', 'ID', 'Max', 'Chromosome', 'Start', 'End']
if args.is_custom_ranges_list():
headers = ['Chromosome', 'Start', 'End', 'Max']
if args.get_include_all():
if args.is_custom_ranges_list():
headers.append('Values')
else:
headers.extend([str(i) for i in range(-1 * up, down + 1)])
yield separator.join(headers) + '\n'
for prediction in predictions:
items = []
if args.is_custom_ranges_list():
items = [
prediction['chrom'],
str(prediction['start']),
str(prediction['end']),
str(prediction['max'])
]
else:
start = prediction['start']
end = prediction['end']
items = [
prediction['commonName'], prediction['name'],
str(prediction['max']), prediction['chrom'],
str(start),
str(end)
]
if args.get_include_all():
items.extend(get_all_values(prediction, size))
yield separator.join(items) + '\n'
def make_values(self, prediction):
values = self.make_base_values(prediction)
return values + get_all_values(prediction, self.size)