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))