remove_tags

Remove XML-style region tags from sequences, either keeping or discarding the enclosed bases. After removal the region is no longer tracked by the pool.

import poolparty as pp
pp.init()

Parameters

Parameter	Type	Default	Description
`pool`	`Pool \| str`	(required)	The Pool to remove tags from. Can also be a plain sequence string.
`region_name`	`str`	(required)	Name of the region whose tags should be removed.
`keep_content`	`bool`	`True`	When `True` the enclosed bases are kept and only the tag markup is stripped. When `False` both the tags and the enclosed bases are deleted, shortening the sequence.
`iter_order`	`int \| None`	`None`	Dimension-name ordering 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 remove_tags() in the API Reference.

Examples

Keep content (default)

Strip the cre tags but leave the four enclosed bases in place.

wt      = pp.from_seq("AAAA<cre>ATCG</cre>TTTT")
cleaned = pp.remove_tags(wt, "cre")
cleaned.print_library()

cleaned: seq_length=12, num_states=1 AAAAATCGTTTT

Drop content (keep_content=False)

Delete both the tags and the enclosed bases, shortening the sequence.

wt      = pp.from_seq("AAAA<cre>ATCG</cre>TTTT")
dropped = pp.remove_tags(wt, "cre", keep_content=False)
dropped.print_library()

dropped: seq_length=8, num_states=1 AAAATTTT

Strip scan tags while keeping another region

After region_scan() the scanning tag remains in every sequence. Use remove_tags to strip it while leaving the cre region tag intact. All seven scan positions collapse to the same visible sequence once the win tag is removed.

wt   = pp.from_seq("AAAA<cre>ATCGATCG</cre>TTTT")
scan = pp.region_scan(wt, tag_name="win", region_length=2,
                      region="cre", mode="sequential")
out  = pp.remove_tags(scan, "win")
out.print_library()

out: seq_length=16, num_states=7 AAAA<cre>ATCGATCG</cre>TTTT
AAAA<cre>ATCGATCG</cre>TTTT
AAAA<cre>ATCGATCG</cre>TTTT
AAAA<cre>ATCGATCG</cre>TTTT
AAAA<cre>ATCGATCG</cre>TTTT ... (7 total)

Remove two regions sequentially

Call remove_tags once per region name to clear multiple tags.

wt    = pp.from_seq("AAAA<left>ATCG</left>GGGG<right>CCCT</right>TTT")
step1 = pp.remove_tags(wt,    "left")
clean = pp.remove_tags(step1, "right")
clean.print_library()

clean: seq_length=19, num_states=1 AAAAATCGGGGGCCCTTTT

See remove_tags().