shuffle_seq

Randomly permute the bases of a sequence, optionally restricting the shuffle to a named region while leaving flanking sequence untouched. Only mode="random" is supported; each draw is an independent permutation.

import poolparty as pp
pp.init()

Parameters

Parameter	Type	Default	Description
`pool`	`Pool \| str`	(required)	The Pool to shuffle. Can also be a plain sequence string.
`region`	`str \| list \| None`	`None`	Restrict the shuffle to a named region or `[start, stop]` interval. Flanking sequences are returned unchanged.
`shuffle_type`	`str`	`"mono"`	`"mono"` randomly permutes individual bases (preserves mononucleotide composition). `"dinuc"` uses an Euler-path shuffle that preserves dinucleotide frequencies.
`prefix`	`str \| None`	`None`	Prefix for auto-generated sequence names.
`mode`	`str`	`'random'`	Only `'random'` is meaningful; each draw produces an independent random permutation.
`num_states`	`int \| None`	`None`	Number of shuffled variants to draw. `None` defaults to 1.
`iter_order`	`int \| None`	`None`	Enumeration order when combined with other pools.
`style`	`str \| None`	`None`	Display style applied to the shuffled result.
`cards`	`dict \| list \| None`	`None`	Design card columns to include in library output.

Note

With shuffle_type="dinuc", the first and last bases are always fixed — this is a mathematical constraint of the Euler-path algorithm used to preserve dinucleotide frequencies.

Note

Only the most commonly used parameters are shown above. For the full parameter list, see shuffle_seq() in the API Reference.

Examples

Shuffle the full sequence

With default num_states (None → 1), each library generation returns one random permutation of all bases. Use a larger num_states to enumerate several shuffles in one call (see below).

wt       = pp.from_seq("ATCGATCG")
shuffled = pp.shuffle_seq(wt, mode="random")
shuffled.print_library()

shuffled: seq_length=8, num_states=1 TGGCAACT ... (stochastic; sequences change each run)

Shuffle only a named region

Only bases inside the tagged region are permuted; flanks are unchanged.

wt       = pp.from_seq("AAAA<cre>ATCGATCG</cre>TTTT")
shuffled = pp.shuffle_seq(wt, region="cre", mode="random")
shuffled.print_library()

shuffled: seq_length=16, num_states=1 AAAA<cre>TGGCAACT</cre>TTTT ... (stochastic; flanks fixed)

Dinucleotide-preserving shuffle

shuffle_type="dinuc" preserves dinucleotide frequencies using an Euler-path algorithm. The first and last bases are always fixed.

The input sequence must have repeated dinucleotides for the shuffle to produce diverse outputs — highly regular sequences like ACGTACGT have only one valid Euler path and will always return the same result.

wt       = pp.from_seq("AACGAACGTTGC")
shuffled = pp.shuffle_seq(wt, shuffle_type="dinuc", num_states=3, mode="random")
shuffled.print_library()

shuffled: seq_length=12, num_states=3 AACGTTGAACGC
AACGAACGTTGC
AAACGTTGACGC

Fixing the number of variants with `num_states`

num_states fixes how many shuffled variants are drawn from the pool in one library generation call.

wt       = pp.from_seq("ATCGATCG")
shuffled = pp.shuffle_seq(wt, num_states=5, mode="random")
shuffled.print_library()

shuffled: seq_length=8, num_states=5 TGGCAACT
AGTACGTC
GTTAAGCC
CACTTGGA
TCATGACG

See shuffle_seq().