api
python.ensembl.ncbi_taxonomy.api
¶
Taxonomy API module
Taxonomy
¶
Contains all the taxonomy related functions over NCBITaxonomy ORM
Attributes:
Name | Type | Description |
---|---|---|
session |
db Session() |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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all_common_ancestors(session, taxon_id_1, taxon_id_2)
classmethod
¶
Returns a tuple of common ancestor node objects shared between taxa
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id_1 |
int
|
Unique taxonomy identifier in database |
required |
taxon_id_2 |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
children(session, taxon_id)
classmethod
¶
Returns taxonomy node object for children nodes
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
fetch_ancestors(session, taxon_id)
classmethod
¶
Returns a tuple of ancestor node objects from taxon_id
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
fetch_node_by_id(session, taxon_id)
classmethod
¶
Returns taxonomy node object by taxon_id
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
fetch_taxon_by_species_name(session, name)
classmethod
¶
Returns first taxonomy object matching name
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
Scientific ncbi_taxa_name.name in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
is_leaf(session, taxon_id)
classmethod
¶
Returns True if taxon_id
is a leaf and False if not
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
is_root(session, taxon_id)
classmethod
¶
Returns True if taxon_id
is a root and False if not
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id |
int
|
Unique taxonomy identifier in database |
required |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
last_common_ancestor(session, taxon_id_1, taxon_id_2)
classmethod
¶
Returns most recent common ancestor node object shared between taxa
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id_1 |
int
|
Unique taxonomy identifier in database |
required |
taxon_id_2 |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
num_descendants(session, taxon_id)
classmethod
¶
Returns number of descendants from taxon_id
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|
parent(session, taxon_id)
classmethod
¶
Returns taxonomy node object for parent node
Parameters:
Name | Type | Description | Default |
---|---|---|---|
taxon_id |
int
|
Unique taxonomy identifier in database |
required |
Raises:
Type | Description |
---|---|
NoResultFound
|
if |
Source code in src/python/ensembl/ncbi_taxonomy/api/utils.py
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|