pylogeny.database module

Connect, access, + manipulate external tree data from a remote SQL server or from an sqlite file.

class pylogeny.database.DatabaseLandscape(ali, starting_tree=None, root=True, operator='SPR')

Bases: pylogeny.landscape.landscape

Abstract the landscape to one comprising a database.

getNode(i)

class pylogeny.database.SQLDatabase(host, user, pw, db)

Bases: pylogeny.database.database

Database object to allow reading from a MySQL database.

__init__(host, user, pw, db)

close()

connect()

getColumns(table)

Return column information for a given table.

getTables()

query(q)

querymany(q, i)

class pylogeny.database.SQLExhaustiveLandscape(dbobj, aliname)

Bases: pylogeny.database.DatabaseLandscape

Abstract the landscape to one comprising an SQL database.

__init__(dbobj, aliname)

Instantiate this landscape.

Parameters:

• dbobj (a database) – a database object
• aliname (a string) – the name of the alignment (table in the database)

exploreRandomTree(i)

exploreTree(i)

getDatabaseNode(i)

class pylogeny.database.SQLiteDatabase(filepath)

Bases: pylogeny.database.database

__init__(filepath)

Instantiate this SQLite database object.

Parameters:filepath (a string) – a path to the file

close()

getColumns(table)

Return column information for a given table.

Parameters:table (a string) – a table name

getTables()

query(q)

querymany(q, i)

class pylogeny.database.SQLiteLandscape(dbobj)

Bases: pylogeny.landscape.landscape

Allow random access of all landscape data from an sqlite file found on the hard disk.

__init__(dbobj)

class pylogeny.database.database

Bases: object

Allow interfacing with a SQL/sqlite database.

__init__()

close()

filterRecords(table, condn)

Get all records from a given table following a condition. The equivalent of calling “SELECT * FROM table WHERE cond”.

Parameters:

• table (a string) – a table name
• condn (a string) – a condition in SQL syntax

Returns:

a list of tuples

getColumns(table)

getHeaders(table)

Get only header names for a given table’s columns.

Parameters:table (a string) – a table name

getRecords(table)

Get all records from a given table in the database. The equivalent of a call “SELECT * FROM table”.

Parameters:table (a string) – a table name Returns:a list of tuples

getRecordsAsDict(table)

Acquires records using getRecords() and then leverages access using a dictionary data structure where keys are headers (column names).

Parameters:table (a string) – a table name Returns:a dictionary (of records as values)

getRecordsColumn(table, col)

Get all data for a single column from records for a table. The equivalent of a call “SELECT col FROM table”.

Parameters:

• table (a string) – a table name
• col (a string) – a column name

Returns:

a list of strings

getTables()

insertRecord(tablename, record)

Insert a single record.

Parameters:

• tablename (a string) – the name of the table
• record (a tuple) – a tuple

insertRecords(tablename, items)

Insert a number of records into a table.

Parameters:

• tablename (a string) – the name of the table
• items (a list of tuples) – a list of record tuples

isEmpty()

Determine if the database is empty.

Returns:a boolean

iterRecords(table)

Get a record, one at a time, from a table in the database.

Parameters:table (a string) – a table name Returns:a generator of records

newTable(tablename, *args)

Create a new table.

Parameters:tablename (a string) – the name of this table

query(q)

querymany(q, i)