def tearDown(self):
# print '\nref: ', self.ref
# print 'query:', self.query
errors = list(sequtils.itemize_errors(self.ref, self.query))
log.debug(sequtils.show_errors(errors))
log.debug('\n' + pprint.pformat(self.expected))
log.debug('\n' + pprint.pformat(errors))
# indices into ref are as expected
self.assertEquals(set(e['i']
for e in errors), set(self.expected.keys()))
# individual positions are as expected
for pos in errors:
self.assertEquals(pos['ref'], self.expected[pos['i']]['ref'])
self.assertEquals(pos['query'], self.expected[pos['i']]['query'])
def action(args):
fieldnames = ['t_name', 'q_name', 'length', 'snp', 'indel']
fieldnames += ['homoindel','compound', 'total', 'sw_zscore']
fieldnames += args.extra_fields.keys()
if args.output_alignment:
fieldnames += ['alignment']
aligns = DictReader(args.aligns)
itemizer = lambda a: dict({'errors':itemize_errors(a['t_seq'], a['q_seq'])}, **a)
aligns = imap(itemizer, aligns)
tallies = DictWriter(args.out,
fieldnames = fieldnames,
extrasaction = 'ignore')
tallies.writeheader()
homopolymers = defaultdict(Counter)
gtceil = 'geq{}'.format(args.homopolymer_max)
# output error counts:
for a in aligns:
# instantiate d with zero counts for each error type
row = {k:0 for k in fieldnames[2:]}
row['q_name'], row['t_name'] = a['q_name'], a['t_name']
row.update(a)
row.update(error_count(a['errors']))
# create total count to output
total = row['snp'] + row['indel'] + row['homoindel'] + row['compound']
row.update({'total':total})
row.update(args.extra_fields)
if args.output_alignment:
row.update({'alignment':show_errors(a['errors'])})
tallies.writerow(row)
log.debug(a['q_name'])
log.debug('\n' + sequtils.format_alignment(a['t_seq'], a['q_seq']))
log.debug(a['q_seq'].replace('-','').replace('=',''))
log.debug(show_errors(a['errors']))
if args.step:
raw_input()
# create homopolymer matrix
for e in a['errors']:
r, q = e['ref'].strip('=-'), e['query'].strip('=-')
# count indels or homoindels; exclude compound errors and snps
base = ''.join(set(r + q))
if len(base) == 1:
ref_count = len(r) if len(r) <= args.homopolymer_max else gtceil
query_count = len(q) if len(q) <= args.homopolymer_max else gtceil
homopolymers['total'][(ref_count, query_count)] += 1
homopolymers[base][(ref_count, query_count)] += 1
# output homopolymer matrix if specified
if args.matrix:
# reference counts in rows, query in column
ii = range(args.homopolymer_max)
margins = ii + [gtceil]
for base in sorted(homopolymers):
args.matrix.writerow([base] + ['q{}'.format(i) for i in ii] + [gtceil])
for i_ref in margins:
cols = [homopolymers[base][i_ref, i_query] for i_query in margins]
args.matrix.writerow(['r{}'.format(i_ref)] + cols)
args.matrix.writerow([''] * 10)
def action(args):
fieldnames = ['t_name', 'q_name', 'length', 'snp', 'indel']
fieldnames += ['homoindel', 'compound', 'total', 'sw_zscore']
fieldnames += args.extra_fields.keys()
if args.output_alignment:
fieldnames += ['alignment']
aligns = DictReader(args.aligns)
itemizer = lambda a: dict(
{'errors': itemize_errors(a['t_seq'], a['q_seq'])}, **a)
aligns = imap(itemizer, aligns)
tallies = DictWriter(args.out,
fieldnames=fieldnames,
extrasaction='ignore')
tallies.writeheader()
homopolymers = defaultdict(Counter)
gtceil = 'geq{}'.format(args.homopolymer_max)
# output error counts:
for a in aligns:
# instantiate d with zero counts for each error type
row = {k: 0 for k in fieldnames[2:]}
row['q_name'], row['t_name'] = a['q_name'], a['t_name']
row.update(a)
row.update(error_count(a['errors']))
# create total count to output
total = row['snp'] + row['indel'] + row['homoindel'] + row['compound']
row.update({'total': total})
row.update(args.extra_fields)
if args.output_alignment:
row.update({'alignment': show_errors(a['errors'])})
tallies.writerow(row)
log.debug(a['q_name'])
log.debug('\n' + sequtils.format_alignment(a['t_seq'], a['q_seq']))
log.debug(a['q_seq'].replace('-', '').replace('=', ''))
log.debug(show_errors(a['errors']))
if args.step:
raw_input()
# create homopolymer matrix
for e in a['errors']:
r, q = e['ref'].strip('=-'), e['query'].strip('=-')
# count indels or homoindels; exclude compound errors and snps
base = ''.join(set(r + q))
if len(base) == 1:
ref_count = len(
r) if len(r) <= args.homopolymer_max else gtceil
query_count = len(
q) if len(q) <= args.homopolymer_max else gtceil
homopolymers['total'][(ref_count, query_count)] += 1
homopolymers[base][(ref_count, query_count)] += 1
# output homopolymer matrix if specified
if args.matrix:
# reference counts in rows, query in column
ii = range(args.homopolymer_max)
margins = ii + [gtceil]
for base in sorted(homopolymers):
args.matrix.writerow([base] + ['q{}'.format(i)
for i in ii] + [gtceil])
for i_ref in margins:
cols = [
homopolymers[base][i_ref, i_query] for i_query in margins
]
args.matrix.writerow(['r{}'.format(i_ref)] + cols)
args.matrix.writerow([''] * 10)
