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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tsalign 5.0.1

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	`781dce9034a796ed27c53ba18a87281e8b6bd41a003423c8b966b962c33cbc81`
MD5	`72130a924e11e790d74688d948d4c492`
BLAKE2b-256	`9715830e6f8f4898ed8ee3a0506c70df1a4d2822cbdd4f95997d8932fcf7de1f`

Algorithm	Hash digest
SHA256	`276547e4bbe2147ac3799cd1f74d5d2b591e839c0fcd7471292a2344f699c1ef`
MD5	`72b7d7e9a42eb8b035da6971704cc021`
BLAKE2b-256	`6ed124bfaeccd492194832c2283f50478d76440fdbad5d78ad94665618350d2b`

Algorithm	Hash digest
SHA256	`6cacc8da6ecd82e65e9ca4e589998377eff3b3c7738b9d46016786ff8f650866`
MD5	`2d8e546b9c6ae8e74854ecbcdab9db6f`
BLAKE2b-256	`e445401114fe716de50476293b402d327a6781e28db8285b09f61509f9bd566a`

Algorithm	Hash digest
SHA256	`0e6d5c0d6aebb4c4cb82f8540034bee9aa144187304beab69c1a31255e592de4`
MD5	`2eb5a10663d39b52c571b7d38c6a3047`
BLAKE2b-256	`b21ffbfd9a31a95584bb3dc06a5a22b36d08ad498084105ef812f99726629ee3`

Algorithm	Hash digest
SHA256	`f97e4e9d022c313806560e3a613a0f50bd3e2db83a04017f8c6c964d53498d4f`
MD5	`32e3a8edafe61ea986666a595c56dbda`
BLAKE2b-256	`dc5057f751db76f38437d002929b16db17513ab36f84142094b5a81c165e24d0`

Algorithm	Hash digest
SHA256	`68b3efe68bdcdf09b9e33138f6c00442bd328ef336c79646109c12d0021b43b3`
MD5	`93c2b4d97184ceb643b4796a0b7ea2d0`
BLAKE2b-256	`86ea651744ef277eecaeb118fa146bd89a8935b31451e0f6f5e10931e8c711e6`

Algorithm	Hash digest
SHA256	`2df7f4defeb1aa6c6317480b7ca1f632cb4747723c96829eb2bef0071aa4c712`
MD5	`da102ba0eec1f1e13077c0392328ae4f`
BLAKE2b-256	`844be3d94892b46d28fa8d6e09a3b86d935bd33486442fa0d98d0134c141080e`

Algorithm	Hash digest
SHA256	`8b9cc3ac48c45ba6b68726a1289b5ae7d7f2922b49768bc42b334b7d463695c5`
MD5	`264f88ebf223db5da869638a1db31fae`
BLAKE2b-256	`4e623f3eedd73b2174d43dfa52ed81208935d94f7cc7df901f6c50ea52b93145`

Algorithm	Hash digest
SHA256	`0530a256fcadb9492e23d9a214a545317d01d9378d9a2524bc04462a97e85ef3`
MD5	`bc6dac3da6cd73af33fb06796e218a94`
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Algorithm	Hash digest
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MD5	`9257ef35761fc11de885fad29ed28dba`
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