slice_seq

Extract a subsequence using Python-style slicing, a named region, or both. When keep_context=True, the sliced content is reassembled into the original flanking context.

import poolparty as pp
pp.init()

Parameters

Parameter	Type	Default	Description
`pool`	`Pool \| str`	(required)	Input pool or sequence string.
`region`	`str \| list \| None`	`None`	Region to slice from. A string selects a named region; a `[start, stop]` pair selects by position. `None` uses the full sequence.
`start`	`int \| None`	`None`	Start index (0-based, Python-style). Applied after region extraction when `region` is set.
`stop`	`int \| None`	`None`	Stop index (exclusive, Python-style).
`step`	`int \| None`	`None`	Step size (Python-style).
`keep_context`	`bool`	`False`	If `True`, reassemble the sliced content back into the original flanking context (prefix + sliced + suffix). Requires `region`.
`iter_order`	`float \| None`	`None`	Enumeration order when combined with other pools.
`prefix`	`str \| None`	`None`	Prefix for the operation node name in the pool graph.
`style`	`str \| None`	`None`	Display style applied to the sliced output.

Note

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

Examples

Slice by position

Extract bases 2–6 from an 8-mer.

pool   = pp.from_seq("ACGTACGT")
sliced = pp.slice_seq(pool, start=2, stop=6)
sliced.print_library()

sliced: seq_length=4, num_states=1 GTAC

Extract a named region

Pull the content of a tagged region into its own pool.

pool = pp.from_seq("AAA<orf>ATGCCC</orf>TTT")
orf  = pp.slice_seq(pool, region="orf")
orf.print_library()

orf: seq_length=6, num_states=1 ATGCCC

Slice within a named region

Combine region with start/stop to slice inside the region. Here, take only the first codon.

pool   = pp.from_seq("AAA<orf>ATGCCC</orf>TTT")
codon1 = pp.slice_seq(pool, region="orf", start=0, stop=3)
codon1.print_library()

codon1: seq_length=3, num_states=1 ATG

Keep context — reassemble flanks

With keep_context=True the sliced region content is placed back into the original flanking sequence.

pool   = pp.from_seq("AAA<orf>ATGCCC</orf>TTT")
sliced = pp.slice_seq(pool, region="orf", start=0, stop=3, keep_context=True)
sliced.print_library()

sliced: seq_length=9, num_states=1 AAAATGTTT

See slice_seq().