def create_scientific_table(nodes_ncbi, names_ncbi):
ranks = nodes_ncbi['rank'].unique()
phylums = get_bind_ids_bact([2, 2323], nodes_ncbi, is_get_child_id=True, rank_ex=ranks[ranks != 'phylum'])['id']
classes = [pd.DataFrame({'phylum': phylum,
'class': get_bind_ids_bact([phylum], nodes_ncbi, is_get_child_id=True,
rank_ex=ranks[ranks != 'class'])['id']})
for phylum in phylums.values]
classes = pd.concat(classes)
orders = [pd.DataFrame({'phylum': row['phylum'],
'class': row['class'],
'order': get_bind_ids_bact([row['class'], row['phylum']], nodes_ncbi, is_get_child_id=True,
rank_ex=ranks[ranks != 'order'])['id']})
for i, row in classes.iterrows()]
orders = pd.concat(orders)
families = [pd.DataFrame({'phylum': row['phylum'],
'class': row['class'],
'order': row['order'],
'family': get_bind_ids_bact([row['order']],
nodes_ncbi, is_get_child_id=True,
rank_ex=ranks[ranks != 'family'])['id']})
for i, row in orders.iterrows()]
families = pd.concat(families)
genuses = [pd.DataFrame({'phylum': row['phylum'],
'class': row['class'],
'order': row['order'],
'family': row['family'],
'genus': get_bind_ids_bact([row['family']],
nodes_ncbi, is_get_child_id=True,
rank_ex=ranks[ranks != 'genus'])['id']})
for i, row in families.iterrows()]
genuses = pd.concat(genuses)
species = [pd.DataFrame({'phylum': row['phylum'],
'class': row['class'],
'order': row['order'],
'family': row['family'],
'genus': row['genus'],
'species': get_bind_ids_bact([row['genus']],
nodes_ncbi, is_get_child_id=True,
rank_ex=ranks[ranks != 'species'])['id']})
for i, row in genuses.iterrows()]
species = pd.concat(species)
names_ncbi_sci = names_ncbi[names_ncbi['class'] == 'scientific name']
species = replace_id_by_name(species, names_ncbi_sci, 'species')
species = replace_id_by_name(species, names_ncbi_sci, 'genus')
species = replace_id_by_name(species, names_ncbi_sci, 'family')
species = replace_id_by_name(species, names_ncbi_sci, 'order')
species = replace_id_by_name(species, names_ncbi_sci, 'class')
species = replace_id_by_name(species, names_ncbi_sci, 'phylum')
return species
def create_all_bact_catalog(nodes_ncbi):
ids = get_bind_ids_bact([2], nodes_ncbi, is_get_child_id=True)
return ids
