annotation
ensembl.io.genomio.annotation
¶
Annotation files processing module.
get_core_data(session, table, match_xrefs=False)
¶
Returns the table descriptions from a core database.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
session
|
Session
|
Session open on a core database. |
required |
table
|
str
|
"gene" or "transcript" table from the core database. |
required |
match_xrefs
|
bool
|
If the IDs do not match, try to match an Xref ID instead. |
False
|
Source code in src/python/ensembl/io/genomio/annotation/update_description.py
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load_descriptions(session, func_file, report=False, do_update=False, match_xrefs=True)
¶
Loads gene and transcript descriptions into a core database.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
session
|
Session
|
Session open on a core database. |
required |
func_file
|
Path
|
JSON file with the annotation information. |
required |
report
|
bool
|
Print the mapping of changes to perform in the standard output. |
False
|
do_update
|
bool
|
Actually update the core database. |
False
|
match_xrefs
|
bool
|
If the IDs do not match, try to match an Xref ID instead. |
True
|
Source code in src/python/ensembl/io/genomio/annotation/update_description.py
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