extract_region

Extract the content of a named region as a new pool. The flanking sequence is discarded and the result contains only the bases inside the region tags.

import poolparty as pp
pp.init()

Parameters

Parameter	Type	Default	Description
`pool`	`Pool \| str`	(required)	Input pool or sequence string containing the named region.
`region_name`	`str`	(required)	Name of the region whose content will be extracted.
`rc`	`bool`	`False`	If `True`, reverse-complement the extracted content.
`iter_order`	`float \| None`	`None`	Iteration priority for downstream multi-pool iteration.
`prefix`	`str \| None`	`None`	Prefix for the operation node name in the pool graph.

Note

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

Examples

Extract a tagged region

Pull the content of the cre region out of a flanked sequence.

bg      = pp.from_seq("AAAA<cre>ATCGATCG</cre>TTTT")
content = pp.extract_region(bg, "cre")
content.print_library()

content: seq_length=8, num_states=1 ATCGATCG

Extract and reverse-complement

Use rc=True to get the reverse complement of the region content — useful for antisense constructs.

bg         = pp.from_seq("AAAA<cre>ATCGATCG</cre>TTTT")
content_rc = pp.extract_region(bg, "cre", rc=True)
content_rc.print_library()

content_rc: seq_length=8, num_states=1 CGATCGAT

Extract from a multi-state pool

When the parent pool has multiple states, each state’s region content is extracted independently.

bg      = pp.from_seq("AAAA<ins>NNNN</ins>TTTT")
filled  = pp.replace_region(bg, pp.from_iupac("NNNN", mode="sequential"),
                            region_name="ins", keep_tags=True)
content = pp.extract_region(filled, "ins")
content.print_library()

content: seq_length=4, num_states=256 AAAA
AAAC
AAAG
AAAT
AACA
... (256 total)

See extract_region().