def write_output(logger, args):
serializer = SeqNameSerializer()
index = None
fields = MARKER_DEF_FIELDS + ("status", "extended_mask")
try:
index = shelve.open(args.index_file, "r")
logger.info("getting extracted sequences")
extracted_seqs = get_extracted_seqs(args.input_file)
if args.align_file:
logger.info("getting sorting order from %r" % (args.align_file))
idx_map = get_sort_idx(args.align_file)
max_idx = max(idx_map.itervalues())
fields += ("marker_indx",)
with nested(open(args.orig_file), open(args.output_file,'w')) as (f, outf):
outf.write("\t".join(fields)+"\n")
reader = csv.DictReader(f, delimiter="\t")
logger.info("looking up against %r" % args.index_file)
for i, r in enumerate(reader):
label = r['label']
old_rs_label = r['rs_label']
mask = r['mask']
try:
seq, alleles = extracted_seqs[label]
except KeyError:
rs_label = extended_mask = 'None'
status = Status.NO_INFO
else:
extended_mask = build_mask(seq, alleles)
key = build_index_key(seq)
tags = index.get(key, [])
n_matches = len(tags)
if n_matches != 1:
logger.warning("%r maps to %d tags: %r" % (label, n_matches, tags))
rs_label = 'None'
status = Status.NO_MATCH if n_matches == 0 else Status.MULTI_MATCH
else:
rs_label, _, _, _ = serializer.deserialize(tags[0])
if old_rs_label == "None":
status = Status.ADDED
else:
status = (Status.CONFIRMED if rs_label == old_rs_label
else Status.REPLACED)
if rs_label == 'None':
rs_label = label
out_r = [label, rs_label, mask, r['allele_a'], r['allele_b'],
status, extended_mask]
if args.align_file:
try:
idx = idx_map[label]
except KeyError:
max_idx += 1
idx = max_idx
out_r.append(str(idx))
outf.write("%s\n" % "\t".join(out_r))
logger.info("processed %d records overall" % (i+1))
finally:
if index:
index.close()
def main(logger, args):
index = None
fd, temp_index_fn = tempfile.mkstemp(dir=args.output_dir)
os.close(fd)
os.remove(temp_index_fn)
try:
index = shelve.open(temp_index_fn, "n", protocol=HP, writeback=True)
with open(args.input_file) as f:
bn = os.path.basename(args.input_file)
logger.info("processing %r" % bn)
reader = csv.reader(f, delimiter="\t")
first_seq_len = None
for i, r in enumerate(reader):
try:
tag = r[3]
seq = r[-1].upper()
if first_seq_len is None:
first_seq_len = len(seq)
elif len(seq) != first_seq_len:
msg = "found input sequences of different length"
logger.critical(msg)
raise ValueError(msg)
except IndexError:
msg = "%r: bad input format, bailing out" % bn
logger.critical(msg)
raise ValueError(msg)
else:
key = build_index_key(seq)
index.setdefault(key, []).append(tag)
if (i + 1) % SYNC_INTERVAL == 0:
logger.info("processed %d records: syncing db" %
(i + 1))
index.sync()
logger.info("processed %d records overall" % (i + 1))
finally:
if index:
index.close()
final_output_fn = os.path.join(
args.output_dir,
"dbsnp_index_%s_%d.db" % (args.reftag, first_seq_len))
os.rename(temp_index_fn, final_output_fn)
logger.info("index stored to: %s" % final_output_fn)
def main(logger, args):
index = None
fd, temp_index_fn = tempfile.mkstemp(dir=args.output_dir)
os.close(fd)
os.remove(temp_index_fn)
try:
index = shelve.open(temp_index_fn, "n", protocol=HP, writeback=True)
with open(args.input_file) as f:
bn = os.path.basename(args.input_file)
logger.info("processing %r" % bn)
reader = csv.reader(f, delimiter="\t")
first_seq_len = None
for i, r in enumerate(reader):
try:
tag = r[3]
seq = r[-1].upper()
if first_seq_len is None:
first_seq_len = len(seq)
elif len(seq) != first_seq_len:
msg = "found input sequences of different length"
logger.critical(msg)
raise ValueError(msg)
except IndexError:
msg = "%r: bad input format, bailing out" % bn
logger.critical(msg)
raise ValueError(msg)
else:
key = build_index_key(seq)
index.setdefault(key, []).append(tag)
if (i+1) % SYNC_INTERVAL == 0:
logger.info("processed %d records: syncing db" % (i+1))
index.sync()
logger.info("processed %d records overall" % (i+1))
finally:
if index:
index.close()
final_output_fn = os.path.join(
args.output_dir, "dbsnp_index_%s_%d.db" % (args.reftag, first_seq_len)
)
os.rename(temp_index_fn, final_output_fn)
logger.info("index stored to: %s" % final_output_fn)
def write_output(logger, args):
serializer = SeqNameSerializer()
index = None
fields = MARKER_DEF_FIELDS + ("status", "extended_mask")
try:
index = shelve.open(args.index_file, "r")
logger.info("getting extracted sequences")
extracted_seqs = get_extracted_seqs(args.input_file)
if args.align_file:
logger.info("getting sorting order from %r" % (args.align_file))
idx_map = get_sort_idx(args.align_file)
max_idx = max(idx_map.itervalues())
fields += ("marker_indx", )
with nested(open(args.orig_file), open(args.output_file,
'w')) as (f, outf):
outf.write("\t".join(fields) + "\n")
reader = csv.DictReader(f, delimiter="\t")
logger.info("looking up against %r" % args.index_file)
for i, r in enumerate(reader):
label = r['label']
old_rs_label = r['rs_label']
mask = r['mask']
try:
seq, alleles = extracted_seqs[label]
except KeyError:
rs_label = extended_mask = 'None'
status = Status.NO_INFO
else:
extended_mask = build_mask(seq, alleles)
key = build_index_key(seq)
tags = index.get(key, [])
n_matches = len(tags)
if n_matches != 1:
logger.warning("%r maps to %d tags: %r" %
(label, n_matches, tags))
rs_label = 'None'
status = Status.NO_MATCH if n_matches == 0 else Status.MULTI_MATCH
else:
rs_label, _, _, _ = serializer.deserialize(tags[0])
if old_rs_label == "None":
status = Status.ADDED
else:
status = (Status.CONFIRMED if rs_label
== old_rs_label else Status.REPLACED)
if rs_label == 'None':
rs_label = label
out_r = [
label, rs_label, mask, r['allele_a'], r['allele_b'],
status, extended_mask
]
if args.align_file:
try:
idx = idx_map[label]
except KeyError:
max_idx += 1
idx = max_idx
out_r.append(str(idx))
outf.write("%s\n" % "\t".join(out_r))
logger.info("processed %d records overall" % (i + 1))
finally:
if index:
index.close()
