Python Bindings for `lib_tsalign`

Python bindings for the template switch aligner. Aligns two DNA sequences while detecting template switches — short-range translocations where a query region is copied from (or aligns to) a different location, possibly on the reverse complement strand.

Installation

pip install tsalign

Quick start

import tsalign

result = tsalign.align("ACGTACGT", "ACGACGT")
print(result.cigar())   # compact alignment string
print(result.stats())   # cost, duration, node counts, …

Aligner options

Create an Aligner once and reuse it for many sequences:

aligner = tsalign.Aligner(
    min_length_strategy="preprocess_lookahead",  # default: "lookahead"
    chaining_strategy="lower_bound",             # default: "none"
    total_length_strategy="maximise",            # default: "maximise"
    no_ts=False,                                 # set True for plain gap-affine
)

result = aligner.align("ACGTACGT", "ACGACGT")

Custom cost configuration

Costs are specified in .tsa format. Use sample_tsa_config/config.tsa as a starting point and consult the main repository README for a description of each parameter.

aligner = tsalign.Aligner(costs_file="sample_tsa_config/config.tsa")
result = aligner.align("ACGTACGT", "ACGACGT")

You can also pass the cost string directly:

with open("my_costs.tsa") as f:
    cost_str = f.read()
aligner = tsalign.Aligner(costs=cost_str)

Restricting the alignment range

Use AlignmentRange to align only a window of the input sequences:

from tsalign import Aligner, AlignmentRange

aligner = Aligner()
result = aligner.align(
    "NNNACGTACGTNNN",
    "ACGACGT",
    range=AlignmentRange(reference_start=3, reference_end=11),
)
print(result.cigar())

Individual start/limit keyword arguments are also accepted when range is not provided:

result = aligner.align(
    "NNNACGTACGTNNN",
    "ACGACGT",
    reference_start=3,
    reference_limit=11,
)

Working with alignment operations

alignment.alignments() returns a typed list of (count, op) pairs:

from tsalign import align, TemplateSwitchEntranceOp, TemplateSwitchExitOp

result = align(reference, query)
for count, op in result.alignments():
    if isinstance(op, TemplateSwitchEntranceOp):
        print(f"Template switch: {op.direction}, descendant={op.descendant}, offset={op.first_offset}")
    elif isinstance(op, TemplateSwitchExitOp):
        print(f"Exit, anti-descendant gap: {op.anti_descendant_gap}")
    else:
        # SimpleAlignmentOp — a basic edit in the primary or secondary track
        print(f"{count}x {op.kind}")

Visualisation

result = tsalign.align(reference, query)
result.viz_template_switches()   # prints ASCII art to stdout

Limiting search resources

result = aligner.align(
    reference,
    query,
    cost_limit=100,       # return None if cost would exceed this
    memory_limit=500_000, # return None if memory exceeds this number of bytes
)
if result is None:
    print("No alignment found within limits")

Accepted sequence types

Any object whose str() representation is a valid DNA string (ACGTN) is accepted — including Bio.Seq:

from Bio.Seq import Seq
result = tsalign.align(Seq("ACGTACGT"), Seq("ACGACGT"))

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Download URL: tsalign-4.1.0.tar.gz
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tsalign 4.1.0

Python Bindings for lib_tsalign

Installation

Quick start

Aligner options

Custom cost configuration

Restricting the alignment range

Working with alignment operations

Visualisation

Limiting search resources

Accepted sequence types

Key dates

1 maintainer

Requires

Classifiers

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Python Bindings for `lib_tsalign`

Algorithm	Hash digest
SHA256	`c768281a5d428e996a9e93ec31956a1909b129779fa53b1f4b29ee6b1b8edbc0`
MD5	`883e8560b9f84680313a7e2af0fecf6f`
BLAKE2b-256	`de1da9ad56fdb5b7e2afd9e4c85bfb19516987245f3a66db2e2b7cc1cd368e5d`

Algorithm	Hash digest
SHA256	`4929c5109cc613893f14167c618470b5079cf6cf21dba3fb4348678eed020221`
MD5	`b8bb4983b29e82456be353b87bb299ab`
BLAKE2b-256	`71ad6a118d50d4f4d3eb4c5d70d48068f4b9f2f1df8bdfd36a132d645d2ef256`

Algorithm	Hash digest
SHA256	`c7169b49732b14cb929a3573f75805f5d88ecdc87271004a8efbceb69df93dc3`
MD5	`80177400abbe51edd5ee57e38b00d508`
BLAKE2b-256	`aba69acf6a0c601613d3ca05905b2393041fea60add6f767412e8ecdeb43d8a0`

Algorithm	Hash digest
SHA256	`fd9a774ff2a1a0f67d3c1663b9b262b74629eccd5aee2c9056df9663320c10e5`
MD5	`7279d12cffd68733822539fb304665e7`
BLAKE2b-256	`5c26a2972812f7f70736724f6e78da0aaabddc55a41eb7fd8ef2b347133c22ad`

Algorithm	Hash digest
SHA256	`72f920a49c8478f426da19bfd0f3f6a1a12de5eeabf401f87a506877ad789ecd`
MD5	`21083a7c26b018966a936188fbe58cdd`
BLAKE2b-256	`415e557deea84ffe7e694417cceb727fc938fb73a84e8da5971bd978a07d8134`

Algorithm	Hash digest
SHA256	`a509bcd678f0b5e29fa0dc3cc91234422f949e656c3368991f00dc4b00adce32`
MD5	`c4dba1b7c5b59aa1a352da138fcf5dbf`
BLAKE2b-256	`38ba0f3813d74d83c8fbf2e34e763de7c55a5b85641b1082e1efb17f085bf30e`

Algorithm	Hash digest
SHA256	`d1e96defd17cf7d4957b5b59982a1ba380ef16fe581e35911726ef6b7ec55c9b`
MD5	`233057ca389fe847e177d52bd8b3b541`
BLAKE2b-256	`3009cbf6a67d95808f28e79d045bc002e9b461a305313088ef25dd0f9dd59463`

Algorithm	Hash digest
SHA256	`45174790e67d75f2fdccc13622cba02dad072d2ec30d913e3695c6beeb6ab2b3`
MD5	`14516fa6aa45d96006ccc56c1a5829a7`
BLAKE2b-256	`4eb65f6917c33d169fee6d3a8d8d93c5138b9320bd3e64b09e6a767a5d7bb17e`

Algorithm	Hash digest
SHA256	`88f18e022f73777456851d268cbcc5780a68389336e43659ad22a8a07de67f69`
MD5	`45aec1b8ad5433efc430b3a11ff2247e`
BLAKE2b-256	`f0f52994900a857efbdaaef345d2e60fccc93f8e3ae5e17b5f8d7202fee1c419`

Algorithm	Hash digest
SHA256	`884b5e0d5efa78750182a8e5e748f2283df4cc82f4755275695f059027a7e620`
MD5	`1c8c6b1402d1cc1188f724575e43bc71`
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