Sample an alignment to a fixed length¶
Let’s load in an alignment of rodents to use in the examples.
How to sample the first n
positions of an alignment¶
We can use the fixed_length
app to sample an alignment to a fixed length. By default, it will sample from the beginning of an alignment, the argument length=20
specifies how many positions to sample.
How to sample n
positions from within an alignment¶
Creating the fixed_length
app with the argument start=x
specifies that the sampled sequence should begin x
positions into the alignment.
How to sample n
positions randomly from within an alignment¶
The start position can be selected at random with random=True
. An optional seed
can be provided to ensure the same start position is used when the app is called.