diff --git a/dsmz-match.py b/dsmz-match.py
index 8294da61e1dc5c263114f51282886622876099d4..03379ddf7af2cc20d73cb3de90963a40761a5fcf 100755
--- a/dsmz-match.py
+++ b/dsmz-match.py
@@ -10,12 +10,13 @@ import collections
class NCBITaxon:
- def __init__(self, taxid, rank):
+ def __init__(self, taxid, rank, division_id):
self.taxid = taxid
self.rank = rank
+ self.division_id = division_id
- def q(self, taxid=None, rank=None):
- return (taxid is None or taxid == self.taxid) and (rank is None or rank == self.rank)
+ def q(self, taxid=None, rank=None, division_id='0'):
+ return (taxid is None or taxid == self.taxid) and (rank is None or rank == self.rank) and (division_id is None or division_id == self.division_id)
class NCBIName:
@@ -32,9 +33,10 @@ def read_ncbi_nodes(filename):
with open(filename) as f:
for line in f:
cols = line.split('\t|\t')
- taxid = cols[0]
+ taxid = 'ncbi:' + cols[0]
rank = cols[2]
- result[taxid] = NCBITaxon(taxid, rank)
+ division_id = cols[4]
+ result[taxid] = NCBITaxon(taxid, rank, division_id)
return result
@@ -43,7 +45,7 @@ def read_ncbi_names(nodes, filename):
with open(filename) as f:
for line in f:
cols = line.split('\t|\t')
- taxid = cols[0]
+ taxid = 'ncbi:' + cols[0]
name = cols[1]
name_type = cols[3].replace('\t|\n', '')
result[name] = NCBIName(nodes[taxid], name_type)
@@ -53,6 +55,7 @@ def read_ncbi_names(nodes, filename):
class BacDiveEntry:
def __init__(self, ncbi_taxa, filename):
self.filename = filename
+ self.bacdive_id = os.path.basename(filename).replace('.xml', '')
self.root = ET.parse(filename).getroot()
self.strain_number = []
self.species = None
@@ -66,7 +69,7 @@ class BacDiveEntry:
self.strain_number = tuple(self._get_strain_numbers())
self._set_taxonomy()
self.complete_name = tuple('%s %s' % (self.species, sn) for sn in self.strain_number)
- self.dispatch, self.ncbi_taxid = self._dispatch(ncbi_taxa)
+ self.dispatch, self.ncbi_taxon = self._dispatch(ncbi_taxa)
self.strain_taxid = self._get_strain_taxid()
self.canonical = self._get_canonical()
@@ -133,39 +136,39 @@ class BacDiveEntry:
name = self._match_first(ncbi_taxa, 'no rank')
if name is not None:
- return 'equivalent', name.taxon.taxid
+ return 'equivalent', name.taxon
name = self._match_first(ncbi_taxa, name_type='type material')
if name is not None:
- return 'type-material-of-' + name.taxon.rank, name.taxon.taxid
+ return 'type-material-of-' + name.taxon.rank, name.taxon
rank = 'subspecies' if self.is_subspecies else 'species'
name = self._match(ncbi_taxa, self.species, rank)
if name is not None:
- return 'append-to-' + rank, name.taxon.taxid
+ return 'append-to-' + rank, name.taxon
if rank == 'subspecies':
name = self._match(ncbi_taxa, self.genus, 'species')
if name is not None:
- return 'append-to-species', name.taxon.taxid
+ return 'append-to-species', name.taxon
name = self._match(ncbi_taxa, self.genus, 'genus')
if name is not None:
- return 'append-to-genus', name.taxon.taxid
+ return 'append-to-genus', name.taxon
name = self._match(ncbi_taxa, self.family, 'family')
if name is not None:
- return 'append-to-family', name.taxon.taxid
+ return 'append-to-family', name.taxon
name = self._match(ncbi_taxa, self.ordo, 'order')
if name is not None:
- return 'append-to-order', name.taxon.taxid
+ return 'append-to-order', name.taxon
name = self._match(ncbi_taxa, self.class_, 'class')
if name is not None:
- return 'append-to-class', name.taxon.taxid
+ return 'append-to-class', name.taxon
name = self._match(ncbi_taxa, self.phylum, 'phylum')
if name is not None:
- return 'append-phylum', name.taxon.taxid
+ return 'append-phylum', name.taxon
name = self._match(ncbi_taxa, self.domain, 'superkingdom')
if name is not None:
- return 'append-to-superkingdom', name.taxon.taxid
+ return 'append-to-superkingdom', name.taxon
return 'fail', None
@@ -186,7 +189,7 @@ def line(f, sep, *cols, tail=None):
sys.stderr.write('Reading NCBI taxonomy: %s %s\n' % (NCBI_NODES_FILE, NCBI_NAMES_FILE))
NCBI_TAXA = read_ncbi_names(read_ncbi_nodes(NCBI_NODES_FILE), NCBI_NAMES_FILE)
os.makedirs(OUTPUT_DIR, exist_ok=True)
-with of('dispatch-report.txt') as out_dispatch, of('dsmz-nodes.dmp') as out_nodes, of('dsmz-names.dmp') as out_names, of('warnings.txt') as out_warn:
+with of('dispatch-report.txt') as out_dispatch, of('dsmz-nodes.dmp') as out_nodes, of('dsmz-names.dmp') as out_names, of('bacdive-to-taxid.txt') as out_link, of('warnings.txt') as out_warn:
sys.stderr.write('Reading BacDive entries: %s\n' % INPUT_DIR)
count_entries = 0
count_dispatches = collections.defaultdict(int)
@@ -201,27 +204,30 @@ with of('dispatch-report.txt') as out_dispatch, of('dsmz-nodes.dmp') as out_node
e = BacDiveEntry(NCBI_TAXA, os.path.join(dirpath, fn))
count_entries += 1
count_dispatches[e.dispatch] += 1
- line(out_dispatch, '\t', e.filename, e.dispatch, e.ncbi_taxid)
+ line(out_dispatch, '\t', e.filename, e.dispatch, '' if e.ncbi_taxon is None else e.ncbi_taxon.taxid)
if e.dispatch.startswith('append-to-'):
if e.strain_taxid in new_ids:
line(out_warn, '\t', e.filename, 'duplicate id ' + e.strain_taxid)
continue
+ if e.ncbi_taxon is not None and e.ncbi_taxon.division_id != '0':
+ line(out_warn, '\t', e.filename, 'not bacteria (div %s) (strain %s) (taxid %s)' % (e.ncbi_taxon.division_id, e.strain_taxid, e.ncbi_taxon.taxid))
new_ids.add(e.strain_taxid)
line(out_nodes, '\t|\t',
e.strain_taxid, # taxid
- e.ncbi_taxid, # parent taxid
+ e.ncbi_taxon.taxid, # parent taxid
'no rank', # rank
'', # embl code
- 0, # division id
- 1, # inherited div flag
+ e.ncbi_taxon.division_id, # division id
+ 1, # inherited div flag
11, # genetic code id
- 1, # inherited GC flag
- 0, # mitochondrial genetic code id
- 1, # inherited MGC flag
- 1, # GenBank hidden flag
- 0, # hidden subtree root flag
+ 1, # inherited GC flag
+ 0, # mitochondrial genetic code id
+ 1, # inherited MGC flag
+ 1, # GenBank hidden flag
+ 0, # hidden subtree root flag
'', # comments
tail='\t|')
+ line(out_link, '\t', e.bacdive_id, e.strain_taxid)
count_new_nodes += 1
if e.canonical is None:
line(out_warn, '\t', e.filename, 'no canonical')
@@ -230,9 +236,10 @@ with of('dispatch-report.txt') as out_dispatch, of('dsmz-nodes.dmp') as out_node
line(out_names, '\t|\t', e.strain_taxid, name, '', 'scientific name' if name == e.canonical else 'strain number', tail='\t|')
count_names_of_new_nodes += 1
elif e.dispatch == 'equivalent' or e.dispatch.startswith('type-material-of-'):
+ line(out_link, '\t', e.bacdive_id, e.ncbi_taxon.taxid)
for name in itertools.chain(e.strain_number, e.complete_name):
if name not in NCBI_TAXA:
- line(out_names, '\t|\t', e.ncbi_taxid, name, '', 'strain number', tail='\t|')
+ line(out_names, '\t|\t', e.ncbi_taxon.taxid, name, '', 'strain number', tail='\t|')
count_new_synonyms += 1
sys.stderr.write('Entries: %d\n' % count_entries)
sys.stderr.write('Dispatches:\n')