def action(args):
logging.info("Loading taxtable")
with args.search_taxtable as fp:
full_taxonomy = taxtable.read(fp)
logging.info("Loading chosen sequence metadata")
chosen_taxonomy = copy.deepcopy(full_taxonomy)
chosen_taxonomy.populate_from_seqinfo(args.chosen_seqinfo)
chosen_taxonomy.prune_unrepresented()
logging.info("loading full sequence metadata")
full_taxonomy.populate_from_seqinfo(args.search_seqinfo)
# Find lonely
nodes = [i for i in chosen_taxonomy if i.rank == args.lonely_rank]
lonely_nodes = [i for i in nodes if is_lonely(i)]
additional_reps = set()
futs = []
with futures.ThreadPoolExecutor(args.threads) as executor:
for node in lonely_nodes:
futs.append(executor.submit(fill_lonely_worker,
node.tax_id,
node.at_rank(args.parent_rank).tax_id, full_taxonomy, args.search_fasta,
n_reps=args.number_of_reps))
while futs:
try:
done, pending = futures.wait(futs, 1, futures.FIRST_COMPLETED)
futs = set(pending)
for f in done:
if f.exception():
raise f.exception()
additional_reps |= f.result()
sys.stderr.write("{0:6d}/{1:6d} complete \r".format(len(lonely_nodes) - len(pending),
len(lonely_nodes)))
except futures.TimeoutError:
pass # Keep waiting
except:
logging.exception("Caught error in child thread - exiting")
executor.shutdown(False)
raise
logging.info("%d additional references", len(additional_reps))
with open(args.chosen_fasta) as fp, args.output as ofp:
shutil.copyfileobj(fp, ofp)
wrap.esl_sfetch(args.search_fasta, additional_reps, ofp)
with args.chosen_seqinfo as fp, args.output_seqinfo as ofp, \
args.search_seqinfo as sub_fp:
fp.seek(0)
r = csv.DictReader(fp)
w = csv.DictWriter(ofp, r.fieldnames, quoting=csv.QUOTE_NONNUMERIC, lineterminator='\n')
w.writeheader()
w.writerows(r)
args.search_seqinfo.seek(0)
for row in csv.DictReader(sub_fp):
if row['seqname'] in additional_reps:
w.writerow(row)
def action(args):
with args.taxtable as fp:
tax = taxtable.read(fp)
with args.extra_nodes_csv:
reader = csv.DictReader(args.extra_nodes_csv)
missing_fields = frozenset(['tax_id', 'tax_name', 'rank', 'parent_id'
]) - frozenset(reader.fieldnames)
if missing_fields:
raise IOError("Missing expected fields: {0}".format(
','.join(missing_fields)))
for row in reader:
if row['tax_id'] in tax.index:
logging.warn(
"tax_id %s already represented in taxtable. [row %d]",
row['tax_id'], reader.line_num)
continue
parent_id = row['parent_id']
rank = row['rank']
try:
parent_node = tax.get_node(parent_id)
except ValueError:
raise ValueError(
"Parent {parent_id} of {tax_id}[{tax_name}] not found.".
format(**row))
if rank not in tax.ranks:
add_rank(tax, parent_node, rank)
node = taxtable.TaxNode(tax_id=row['tax_id'],
name=row['tax_name'],
rank=rank)
parent_node.add_child(node)
logging.info("Added %s %s[%s] below %s %s[%s]", node.rank,
node.tax_id, node.name, parent_node.rank,
parent_node.tax_id, parent_node.name)
tax.write_taxtable(args.out_file)
return 0
def action(args):
with args.taxtable as fp:
tax = taxtable.read(fp)
with args.extra_nodes_csv:
reader = csv.DictReader(args.extra_nodes_csv)
missing_fields = frozenset(
['tax_id', 'tax_name', 'rank', 'parent_id']) - frozenset(reader.fieldnames)
if missing_fields:
raise IOError("Missing expected fields: {0}".format(
','.join(missing_fields)))
for row in reader:
if row['tax_id'] in tax.index:
logging.warn("tax_id %s already represented in taxtable. [row %d]",
row['tax_id'], reader.line_num)
continue
parent_id = row['parent_id']
rank = row['rank']
try:
parent_node = tax.get_node(parent_id)
except ValueError:
raise ValueError(
"Parent {parent_id} of {tax_id}[{tax_name}] not found.".format(**row))
if rank not in tax.ranks:
add_rank(tax, parent_node, rank)
node = taxtable.TaxNode(
tax_id=row['tax_id'], name=row['tax_name'], rank=rank)
parent_node.add_child(node)
logging.info(
"Added %s %s[%s] below %s %s[%s]",
node.rank, node.tax_id, node.name,
parent_node.rank, parent_node.tax_id, parent_node.name)
tax.write_taxtable(args.out_file)
return 0
def add_clusters_to_refpkg(refpkg, **kwargs):
with refpkg.open_resource('taxonomy') as tax_fp:
tax = taxtable.read(tax_fp)
with refpkg.open_resource('seq_info') as sinfo_fp:
reader = csv.DictReader(sinfo_fp)
sinfo = list(reader)
# Annotate
add_cluster_taxids(tax, sinfo, **kwargs)
with util.ntf(prefix='seq_info-', suffix='.csv') as seqinfo_tf, \
util.ntf(prefix='taxonomy-', suffix='.csv') as tax_tf:
w = csv.DictWriter(seqinfo_tf, reader.fieldnames)
w.writeheader()
w.writerows(sinfo)
seqinfo_tf.close()
tax.write_taxtable(tax_tf)
tax_tf.close()
refpkg.start_transaction()
refpkg.update_file('seq_info', seqinfo_tf.name)
refpkg.update_file('taxonomy', tax_tf.name)
refpkg.commit_transaction()
def action(args):
log_writer = None
if args.log:
log_writer = csv.DictWriter(args.log, ['seqname', 'orig_tax_id',
'renamed_tax_id', 'renamed_tax_name', 'best_hit', 'pct_id',
'applied'], quoting=csv.QUOTE_NONNUMERIC, lineterminator='\n')
log_writer.writeheader()
# Load all tax_ids
with args.taxtable as fp:
new_tax = taxtable.read(fp)
with args.seq_info as fp:
new_seq_info = {row['seqname']: row for row in csv.DictReader(fp)}
with args.refpkg.open_resource('aln_fasta') as fp:
ref_sequences = [ungap(i) for i in SeqIO.parse(fp, 'fasta')]
with args.refpkg.open_resource('seq_info') as fp:
ref_seq_info_reader = csv.DictReader(fp)
ref_seq_info = {row['seqname']: row for row in ref_seq_info_reader}
with args.refpkg.open_resource('taxonomy') as fp:
ref_taxonomy = taxtable.read(fp)
search = functools.partial(uclust.search,
pct_id=args.percent_id,
search_pct_id=0.9, quiet=True)
# Search the sequences from the reference package against the input sequences
with util.as_fasta(ref_sequences) as ref_fasta_path, util.ntf(prefix='uclust') as tf:
search(args.fasta_file, ref_fasta_path, tf.name)
input_records = uclust.parse_uclust_out(i for i in tf if i.startswith('H'))
# Also search sequences from the reference package against themselves
# TODO: decide if we want to use this
#with util.ntf(prefix='uclust') as self_tf:
#search(ref_fasta_path, ref_fasta_path, self_tf.name, maxaccepts=10)
#ref_records = uclust.parse_uclust_out(i for i in self_tf if i.startswith('H'))
## Drop self-hits
#ref_records = (i for i in ref_records if i.query_label != i.target_label)
#grouped = itertools.groupby(ref_records, operator.attrgetter('query_label'))
#best_hit_id = dict((g, max(i.pct_id for i in v)) for g, v in grouped)
for record in input_records:
ref_si = ref_seq_info[record.query_label]
target_si = new_seq_info[record.target_label]
#if record.pct_id > best_hit_id.get(record.query_label, 0.0):
tax_id = target_si['tax_id']
node = new_tax.get_node(tax_id)
if log_writer:
log_record = {'seqname': record.query_label,
'best_hit': record.target_label,
'pct_id': record.pct_id,
'orig_tax_id': ref_si['tax_id'],
'renamed_tax_id': node.tax_id,
'renamed_tax_name': node.name,
'applied': not ref_si['tax_id'] or args.conflict_action == 'replace'}
log_writer.writerow(log_record)
logging.info('Naming %s %s[%s,%s] based on %s (%.2f%%)', ref_si['seqname'],
node.name, node.tax_id, node.rank, record.target_label, record.pct_id)
if ref_si['tax_id'] and ref_si['tax_id'] != tax_id:
old_node = ref_taxonomy.get_node(ref_si['tax_id'])
logging.warn('Already named: %s[%s,%s]%s',
old_node.name, old_node.tax_id, old_node.rank,
' - replacing' if args.conflict_action == 'replace' else '')
if not ref_si['tax_id'] or args.conflict_action == 'replace':
ref_si['tax_id'] = target_si['tax_id']
if tax_id not in ref_taxonomy.index:
add_to_taxonomy(ref_taxonomy, node)
# Write updated taxtable, seqinfo
with util.ntf(prefix='taxonomy-', suffix='.csv') as new_tax, \
util.ntf(prefix='seq_info-', suffix='.csv') as new_seq_info:
ref_taxonomy.write_taxtable(new_tax)
new_tax.close()
w = csv.DictWriter(new_seq_info, ref_seq_info_reader.fieldnames)
w.writeheader()
w.writerows(ref_seq_info.values())
new_seq_info.close()
args.refpkg.start_transaction()
args.refpkg.update_file('taxonomy', new_tax.name)
args.refpkg.update_file('seq_info', new_seq_info.name)
args.refpkg.commit_transaction()
def action(args):
logging.info("Loading taxtable")
with args.search_taxtable as fp:
full_taxonomy = taxtable.read(fp)
logging.info("Loading chosen sequence metadata")
chosen_taxonomy = copy.deepcopy(full_taxonomy)
chosen_taxonomy.populate_from_seqinfo(args.chosen_seqinfo)
chosen_taxonomy.prune_unrepresented()
logging.info("loading full sequence metadata")
full_taxonomy.populate_from_seqinfo(args.search_seqinfo)
if args.exclude_taxids:
for e in args.exclude_taxids:
e = e.strip()
logging.info('ignoring tax_id {}'.format(e))
full_taxonomy.get_node(e).remove_subtree()
# Find lonely
nodes = [i for i in chosen_taxonomy if i.rank == args.lonely_rank]
lonely_nodes = [i for i in nodes if is_lonely(i)]
additional_reps = set()
futs = []
with futures.ThreadPoolExecutor(args.threads) as executor:
for node in lonely_nodes:
futs.append(
executor.submit(fill_lonely_worker,
node.tax_id,
node.at_rank(args.parent_rank).tax_id,
full_taxonomy,
args.search_fasta,
n_reps=args.number_of_reps))
while futs:
try:
done, pending = futures.wait(futs, 1, futures.FIRST_COMPLETED)
futs = set(pending)
for f in done:
if f.exception():
raise f.exception()
additional_reps |= f.result()
sys.stderr.write("{0:6d}/{1:6d} complete \r".format(
len(lonely_nodes) - len(pending), len(lonely_nodes)))
except futures.TimeoutError:
pass # Keep waiting
except:
logging.exception("Caught error in child thread - exiting")
executor.shutdown(False)
raise
if args.include_taxids:
for t in args.include_taxids:
t = t.strip()
logging.info('including tax_id {}'.format(t))
for s in set(full_taxonomy.get_node(t).subtree_sequence_ids()):
logging.info('sequence {}'.format(s))
additional_reps.add(s)
logging.info("%d additional references", len(additional_reps))
with open(args.chosen_fasta) as fp, args.output as ofp:
shutil.copyfileobj(fp, ofp)
wrap.esl_sfetch(args.search_fasta, additional_reps, ofp)
with args.chosen_seqinfo as fp, args.output_seqinfo as ofp, \
args.search_seqinfo as sub_fp:
fp.seek(0)
r = csv.DictReader(fp)
w = csv.DictWriter(ofp,
r.fieldnames,
quoting=csv.QUOTE_NONNUMERIC,
lineterminator='\n')
w.writeheader()
w.writerows(r)
args.search_seqinfo.seek(0)
for row in csv.DictReader(sub_fp):
if row['seqname'] in additional_reps:
w.writerow(row)
def action(args):
log_writer = None
if args.log:
log_writer = csv.DictWriter(args.log, [
'seqname', 'orig_tax_id', 'renamed_tax_id', 'renamed_tax_name',
'best_hit', 'pct_id', 'applied'
],
quoting=csv.QUOTE_NONNUMERIC,
lineterminator='\n')
log_writer.writeheader()
# Load all tax_ids
with args.taxtable as fp:
new_tax = taxtable.read(fp)
with args.seq_info as fp:
new_seq_info = {row['seqname']: row for row in csv.DictReader(fp)}
with args.refpkg.open_resource('aln_fasta') as fp:
ref_sequences = [ungap(i) for i in SeqIO.parse(fp, 'fasta')]
with args.refpkg.open_resource('seq_info') as fp:
ref_seq_info_reader = csv.DictReader(fp)
ref_seq_info = {row['seqname']: row for row in ref_seq_info_reader}
with args.refpkg.open_resource('taxonomy') as fp:
ref_taxonomy = taxtable.read(fp)
search = functools.partial(uclust.search,
pct_id=args.percent_id,
search_pct_id=0.9,
quiet=True)
# Search the sequences from the reference package against the input sequences
with util.as_fasta(ref_sequences) as ref_fasta_path, util.ntf(
prefix='uclust') as tf:
search(args.fasta_file, ref_fasta_path, tf.name)
input_records = uclust.parse_uclust_out(i for i in tf
if i.startswith('H'))
# Also search sequences from the reference package against themselves
# TODO: decide if we want to use this
#with util.ntf(prefix='uclust') as self_tf:
#search(ref_fasta_path, ref_fasta_path, self_tf.name, maxaccepts=10)
#ref_records = uclust.parse_uclust_out(i for i in self_tf if i.startswith('H'))
## Drop self-hits
#ref_records = (i for i in ref_records if i.query_label != i.target_label)
#grouped = itertools.groupby(ref_records, operator.attrgetter('query_label'))
#best_hit_id = dict((g, max(i.pct_id for i in v)) for g, v in grouped)
for record in input_records:
ref_si = ref_seq_info[record.query_label]
target_si = new_seq_info[record.target_label]
#if record.pct_id > best_hit_id.get(record.query_label, 0.0):
tax_id = target_si['tax_id']
node = new_tax.get_node(tax_id)
if log_writer:
log_record = {
'seqname':
record.query_label,
'best_hit':
record.target_label,
'pct_id':
record.pct_id,
'orig_tax_id':
ref_si['tax_id'],
'renamed_tax_id':
node.tax_id,
'renamed_tax_name':
node.name,
'applied':
not ref_si['tax_id'] or args.conflict_action == 'replace'
}
log_writer.writerow(log_record)
logging.info('Naming %s %s[%s,%s] based on %s (%.2f%%)',
ref_si['seqname'], node.name, node.tax_id, node.rank,
record.target_label, record.pct_id)
if ref_si['tax_id'] and ref_si['tax_id'] != tax_id:
old_node = ref_taxonomy.get_node(ref_si['tax_id'])
logging.warn(
'Already named: %s[%s,%s]%s', old_node.name,
old_node.tax_id, old_node.rank, ' - replacing'
if args.conflict_action == 'replace' else '')
if not ref_si['tax_id'] or args.conflict_action == 'replace':
ref_si['tax_id'] = target_si['tax_id']
if tax_id not in ref_taxonomy.index:
add_to_taxonomy(ref_taxonomy, node)
# Write updated taxtable, seqinfo
with util.ntf(prefix='taxonomy-', suffix='.csv') as new_tax, \
util.ntf(prefix='seq_info-', suffix='.csv') as new_seq_info:
ref_taxonomy.write_taxtable(new_tax)
new_tax.close()
w = csv.DictWriter(new_seq_info, ref_seq_info_reader.fieldnames)
w.writeheader()
w.writerows(ref_seq_info.values())
new_seq_info.close()
args.refpkg.start_transaction()
args.refpkg.update_file('taxonomy', new_tax.name)
args.refpkg.update_file('seq_info', new_seq_info.name)
args.refpkg.commit_transaction()