def testMapHeaders(self):
"""
Gets header(s) and info from each file
"""
fname = path.join(summary_testfiles, '{}_gatk.variant_function').format(control)
header_ids = {0: 'var_type_1',
1: 'gene',
7: 'zygosity',
12: 'rsid_1',
8: 'GATK_Score'}
variant_idx = [2, 3, 4, 5, 6]
out = summary.map_headers(fname, header_ids, variant_idx)
out = list(out)
self.assertEqual(len(out), 1713)
header_keys = set(header_ids.values())
# confirm that all keys in header_ids are contained in each row of the output
for pos, data in out:
self.assertFalse(header_keys - set(data.keys()))
def action(args):
(infiles, ) = args.infiles
headers = ['Position'] + variant_headers[3:5] + [
'Gene',
'dbSNP_ID',
'Variant_Type',
'Transcripts',
'Clinically_Flagged',
'NCI60',
'Cosmic',
'Segdup',
'Polyphen',
'Sift',
'Mutation_Taster',
'Gerp',
'1000g_ALL',
'EVS_esp6500_ALL',
'1000g_AMR',
'EVS_esp6500_AA',
'1000g_EUR',
'EVS_esp6500_EU',
'1000g_ASN',
'1000g_AFR']
# accumulate data from all input files for each variant
output = defaultdict(dict)
for fname in infiles:
_, file_type = path.basename(fname).split('.', 1)
try:
header_ids, var_key_ids = file_types[file_type]
except KeyError:
log.warning('no match: %s' % fname)
if args.strict:
sys.exit(1)
continue
for var_key, data in map_headers(fname, header_ids, var_key_ids):
output[var_key].update(data)
writer = csv.DictWriter(args.outfile,
fieldnames = headers,
quoting = csv.QUOTE_MINIMAL,
extrasaction = 'ignore',
delimiter='\t')
writer.writeheader()
sort_key = lambda row: [(row[k]) for k in ['chr','start','stop']]
# write each row (with all data aggregated), modifying fields as necessary
for data in sorted(output.values(), key = sort_key):
# modify any specific fields here
data['Variant_Type'] = data.get('var_type_2') if data.get('var_type_2','').strip() else data.get('var_type_1')
data['Gene'], data['Transcripts'] = munge_gene_and_Transcripts(data)
data['dbSNP_ID']=data.get('rsid_1') or data.get('rsid_2')
data['1000g_ALL']=data.get('1000g_ALL') or -1
data['1000g_AMR']=data.get('1000g_AMR') or -1
data['1000g_ASN']=data.get('1000g_ASN') or -1
data['1000g_AFR']=data.get('1000g_AFR') or -1
data['1000g_EUR']=data.get('1000g_EUR') or -1
data['EVS_esp6500_ALL']=data.get('EVS_esp6500_ALL') or -1
data['EVS_esp6500_AA']=data.get('EVS_esp6500_AA') or -1
data['EVS_esp6500_EU']=data.get('EVS_esp6500_EU') or -1
writer.writerow(data)