skbio.alignment.TabularMSA.sort

TabularMSA.sort(level=None, ascending=True)[source]

Sort sequences by index label in-place.

Parameters
  • level (int or object, optional) – Index level to sort on when index is a pd.MultiIndex. Does nothing otherwise.

  • ascending (bool, optional) – If False, sort in descending (i.e., reverse) order.

Notes

This is a passthrough to pd.Series.sort_index internally.

Examples

Create a TabularMSA object with sequence identifiers as index labels:

>>> from skbio import DNA, TabularMSA
>>> seqs = [DNA('ACG', metadata={'id': 'c'}),
...         DNA('AC-', metadata={'id': 'b'}),
...         DNA('AC-', metadata={'id': 'a'})]
>>> msa = TabularMSA(seqs, minter='id')
>>> msa
TabularMSA[DNA]
---------------------
Stats:
    sequence count: 3
    position count: 3
---------------------
ACG
AC-
AC-
>>> msa.index
Index(['c', 'b', 'a'], dtype='object')

Sort the sequences in alphabetical order by index label:

>>> msa.sort()
>>> msa
TabularMSA[DNA]
---------------------
Stats:
    sequence count: 3
    position count: 3
---------------------
AC-
AC-
ACG
>>> msa.index
Index(['a', 'b', 'c'], dtype='object')

Note that since the sort is in-place, the TabularMSA object is modified (a new object is not returned).