def import_cmd(conn: sqlite3.Connection,
feature=str,
name=str,
path=str,
**kwargs):
"""Import command for wordsets only
This following VQL command:
`IMPORT WORDSETS "gene.txt" AS boby`
will execute :
`import_cmd(conn, "WORDSETS", "gene.txt")`
Args:
conn (sqlite3.Connection): sqlite3 connection
feature (str): "WORDSETS" (Name of the SQL table)
name (str): name of the set
path (str): a filepath
Returns:
dict: `{success: <boolean>}`
Raises:
vql.VQLSyntaxError
"""
accepted_features = ("wordsets", )
if feature.lower() not in accepted_features:
raise vql.VQLSyntaxError(f"option {feature} doesn't exists")
if not os.path.isfile(path):
raise vql.VQLSyntaxError(f"{path} doesn't exists")
affected_rows = sql.import_wordset_from_file(conn, name, path)
return {"success": (affected_rows is not None)}
def bed_cmd(conn: sqlite3.Connection, path: str, target: str, source: str,
**kwargs):
"""Create a new selection from a bed file
This following VQL command:
`CREATE boby FROM variants INTERSECT "path/to/file.bed"`
will execute :
`bed_cmd(conn, "path/to/file.bed", "boby", "source")`
Args:
conn (sqlite3.Connection): sqlite3 connection
path (str): path to bedfile ( a 3 columns files with chr, start, end )
target (str): target selection table
source (str): source selection table
Returns:
dict: {"id": id of last line inserted} if lines have been inserted,
or empty dict in case of error
Raises:
vql.VQLSyntaxError
"""
if not os.path.isfile(path):
raise vql.VQLSyntaxError(f"{path} doesn't exists")
# bed_intervals: chrom, start, end, name, etc. keys in each interval
# see also cutevariant/core/reader/bedreader.py
selection_id = sql.create_selection_from_bed(conn, source, target,
BedReader(path))
return dict() if selection_id is None else {"id": selection_id}
def show_cmd(conn: sqlite3.Connection, feature: str, **kwargs):
"""Show command display information from a SHOW query
This following VQL command:
`SHOW variants`
will execute :
`show_cmd(conn, "variants")`
Args:
conn (sqlite3.Connection): sqlite3 connection
feature (str): Requested feature type of items (Name of the SQL table);
Lower case features are also accepted.
can be: `"selections", "fields", "samples", "wordsets"`
Yields:
(generator[dict]): Items according to requested feature.
Raises:
vql.VQLSyntaxError
"""
accepted_features = {
"selections": sql.get_selections,
"fields": sql.get_fields,
"samples": sql.get_samples,
"wordsets": sql.get_wordsets,
}
# Cast in lower case
feature = feature.lower()
if feature not in accepted_features:
raise vql.VQLSyntaxError(f"option {feature} doesn't exists")
for item in accepted_features[feature](conn):
yield item
def drop_cmd(conn: sqlite3.Connection, feature: str, name: str, **kwargs):
"""Drop selection or set from database
This following VQL commands::
DROP selections boby
DROP wordsets mygene
will execute::
drop_cmd(conn, "selections", "boby")
drop_cmd(conn, "wordsets", "boby")
Args:
conn (sqlite3.Connection): sqlite connection
feature (str): selections or wordsets (Names of the SQL tables).
Lower case features are also accepted.
name (str): name of the selection or name of the wordset
Returns:
dict: {"success": <boolean>}; True if deletion is ok, False otherwise.
Raises:
vql.VQLSyntaxError
"""
accept_features = ("selections", "wordsets")
# Cast to lower case
feature = feature.lower()
if feature not in accept_features:
raise vql.VQLSyntaxError(f"{feature} doesn't exists")
affected_lines = sql.delete_by_name(conn, name, table_name=feature)
return {"success": (affected_lines > 0)}
def create_command_from_obj(conn, vql_obj: dict):
"""Create command function from vql object according to its "cmd" key
cmd authorized:
- select_cmd
- count_cmd
- drop_cmd
- create_cmd
- set_cmd
- bed_cmd
- show_cmd
- import_cmd
Warning:
Use :meth:`execute` instead, that is a wrapper to this function.
Examples:
If you want to create a select_cmd function, pass a vql_obj like this one:
.. code-block:: python
{
"cmd": "select_cmd",
"fields": ["chr", "pos"],
"source": "variants",
"filters": {},
}
Args:
conn (sqlite3.Connection): sqlite3.connection
vql_obj (dict): A VQL object with requested commands at "cmd" key:
`select_cmd, create_cmd, set_cmd, bed_cmd, show_cmd, import_cmd,
drop_cmd, count_cmd`.
A VQL object is dictionary returned by vql.parse.
Returns:
(function): Function object wrapping the given vql_object.
"""
command = vql_obj["cmd"]
if command in globals():
return functools.partial(globals()[command], conn, **vql_obj)
raise vql.VQLSyntaxError(f"cmd {command} doesn't exists")
