def testGetLocation02(self):
"""
Tests integer arguments
"""
loc = get_location(1, 1, 100)
self.assertEquals(loc, 'chr1:1-100')
loc = get_location(1, 1, 1)
self.assertEquals(loc, 'chr1:1')
def testGetLocation01(self):
"""
Tests string arguments
"""
loc = get_location('1', '1', '100')
self.assertEquals(loc, 'chr1:1-100')
loc = get_location('1', '1', '1')
self.assertEquals(loc, 'chr1:1')
def testGetLocation02(self):
"""
Tests integer arguments
"""
loc = ann.get_location(1, 1, 100)
self.assertEquals(loc, 'chr1:1-100')
loc = ann.get_location(1, 1, 1)
self.assertEquals(loc, 'chr1:1')
def testGetLocation01(self):
"""
Tests string arguments
"""
loc = ann.get_location('1', '1', '100')
self.assertEquals(loc, 'chr1:1-100')
loc = ann.get_location('1', '1', '1')
self.assertEquals(loc, 'chr1:1')
def map_headers(fname, header_ids, variant_idx):
"""
Gets header(s) and info from each file
"""
# dict mapping variant keys to columns
with open(fname, 'rU') as infile:
reader = csv.reader(infile, delimiter='\t')
for row in reader:
#adds the value from each position (2,3,4,5,6) to the variant_id
variant_id = tuple(row[i] for i in variant_idx)
#create dict of variants {2:'chr', 3:'start', 4:'stop, 5:'ref', 6:'var'}
variant_dict = dict(zip(variant_headers, variant_id))
#create dict of data from this file; key is included only
#if value is not the empty string
data = dict((key, row[i]) for i, key in header_ids.items() if row[i].strip())
data['Position'] = get_location(**variant_dict)
yield (variant_id, dict(data, **variant_dict))
def map_headers(fname, header_ids, variant_idx):
"""
Gets header(s) and info from each file
"""
# dict mapping variant keys to columns
with open(fname, 'rU') as infile:
reader = csv.reader(infile, delimiter='\t')
for row in reader:
#adds the value from each position (2,3,4,5,6) to the variant_id
variant_id = tuple(row[i] for i in variant_idx)
#create dict of variants {2:'chr', 3:'start', 4:'stop, 5:'ref', 6:'var'}
variant_dict = dict(zip(variant_headers, variant_id))
#create dict of data from this file; key is included only
#if value is not the empty string
data = dict((key, row[i]) for i, key in header_ids.items()
if row[i].strip())
data['Position'] = get_location(**variant_dict)
yield (variant_id, dict(data, **variant_dict))
