Esempio n. 1
0
# column 0; but the column really ought to be chosen by a command line
# argument, either by position or by column name (in header).

name_column = 0

# Extract just the taxon names from the table, as a vector, one entry per row.

ids = []
for row in rows:
    ids.append(row[name_column])

# Invoke the Open Tree TNRS service.
# TBD: consider doing fuzzy matches as well (with a high threshold).  Not
# clear what the user should do for names that don't uniquely resolve.

tnrs_return = opentreelib.tnrs_match_names(ids, do_approximate_matching=False)
# import pprint
# pprint.PrettyPrinter().pprint(tnrs_return)

# Process the wad of stuff that the TNRS returned.  First, index the
# results by taxon name.

name_to_matches = {}
for lump in tnrs_return['results']:
    name_to_matches[lump['id']] = lump['matches']

# Now add the OTT id as a new column at the right side of the table.

for row in rows:
    name = row[name_column]
    if name in name_to_matches:
Esempio n. 2
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def unique_ott_id(name):
    tnrs_result = opentreelib.tnrs_match_names([name])
    ottid = tnrs_result['results'][0]['matches'][0]['ot:ottId']
    return ottid
Esempio n. 3
0
# column 0; but the column really ought to be chosen by a command line
# argument, either by position or by column name (in header).

name_column = 0

# Extract just the taxon names from the table, as a vector, one entry per row.

ids = []
for row in rows:
    ids.append(row[name_column])

# Invoke the Open Tree TNRS service.
# TBD: consider doing fuzzy matches as well (with a high threshold).  Not
# clear what the user should do for names that don't uniquely resolve.

tnrs_return = opentreelib.tnrs_match_names(ids, do_approximate_matching=False)
# import pprint
# pprint.PrettyPrinter().pprint(tnrs_return)

# Process the wad of stuff that the TNRS returned.  First, index the
# results by taxon name.

name_to_matches = {}
for lump in tnrs_return['results']:
    name_to_matches[lump['id']] = lump['matches']

# Now add the OTT id as a new column at the right side of the table.

for row in rows:
    name = row[name_column]
    if name in name_to_matches:
Esempio n. 4
0
def unique_ott_id(name):
    tnrs_result = opentreelib.tnrs_match_names([name])
    ottid = tnrs_result['results'][0]['matches'][0]['ot:ottId']
    return ottid