load
ensembl.io.genomio.events.load
¶
Provided a file with events, load them in a core database.
cf the load_events functions for the events tab file format.
EventCollection
¶
Collection of events with loader/writer in various formats.
Source code in src/python/ensembl/io/genomio/events/load.py
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events = []
instance-attribute
¶
add_deletes(genes, release_name='release_name', release_date='release_date')
¶
Add deletion events from a list of deleted genes.
Source code in src/python/ensembl/io/genomio/events/load.py
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load_events(input_file)
¶
Load events from input file. Expected tab file columns: old_id, new_id, event_name, release, release_date
Source code in src/python/ensembl/io/genomio/events/load.py
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load_events_from_gene_diff(input_file, release_name='release_name', release_date='release_date')
¶
Load events from input file from gene_diff.
Source code in src/python/ensembl/io/genomio/events/load.py
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remap_to_ids(map_dict)
¶
Using a mapping dict, remap the to_id of all events.
Raises:
Type | Description |
---|---|
ValueError
|
If there are events without map information. |
Source code in src/python/ensembl/io/genomio/events/load.py
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write_events_to_db(session, update=False)
¶
Insert the events in the core database. A mapping session is created for each different 'release'.
Source code in src/python/ensembl/io/genomio/events/load.py
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write_events_to_file(output_file)
¶
Write the events to a file.
Source code in src/python/ensembl/io/genomio/events/load.py
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IdEvent
dataclass
¶
Simple representation for the events from the input file
Source code in src/python/ensembl/io/genomio/events/load.py
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event
instance-attribute
¶
from_id
instance-attribute
¶
release
instance-attribute
¶
release_date
instance-attribute
¶
to_id
instance-attribute
¶
is_change()
¶
If the event is an update of an existing gene.
Source code in src/python/ensembl/io/genomio/events/load.py
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MapSession
¶
Simple mapping_sessions representation from the input file
Source code in src/python/ensembl/io/genomio/events/load.py
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events = []
instance-attribute
¶
release = release
instance-attribute
¶
release_date = release_date
instance-attribute
¶
add_event(event)
¶
Add an event to this mapping_session
Source code in src/python/ensembl/io/genomio/events/load.py
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main()
¶
Main entrypoint
Source code in src/python/ensembl/io/genomio/events/load.py
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