From db2ddd24fff76bf5c409f386fa450dd5e0c80169 Mon Sep 17 00:00:00 2001 From: Sebastian Schmidt <61014855+sebschmi@users.noreply.github.com> Date: Tue, 19 May 2026 10:50:42 +0300 Subject: [PATCH 1/3] Enhance README with Python bindings and visualisation details Add Python bindings section and update visualisation instructions --- README.md | 38 ++++++++++++++++++++++++++++---------- 1 file changed, 28 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index a46dfa23..5545773d 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,12 @@ Library downloads Library docs + + Python bindings: + Python bindings version + Python bindings downloads + + ## Features @@ -33,6 +39,14 @@ If you ever want to update to a new release, simply run `cargo install tsalign` again. +### Python bindings + +1. Install the python package manager [`pip`](https://pypi.org/project/pip/). + +2. Run `pip install tsalign`. + +3. Refer to [the python bindings README](python_bindings/README.md) for more information. + ### From Source (For Developers) 1. Install the rust toolchain by going to [rustup.rs](https://rustup.rs/) and following the instructions. @@ -91,7 +105,7 @@ This does not pertain the special `|` character if `--use-embedded-rq-ranges` is If you want to compute an alignment without template switches, you can use the `--no-ts` parameter. This can be useful for comparing the optimal template switching alignment with the optimal alignment without template switches. -### Visualisation +### SVG/PNG Visualisation To visualise the alignment, you can use the `tsalign show` subcommand. For an optimal experience, compute both the alignment with template switches and the alignment without template switches. @@ -102,28 +116,27 @@ tsalign align -p pair.fa -o alignment.toml -c sample_tsa_config --memory-limit 1 tsalign align -p pair.fa -o alignment-no-ts.toml -c sample_tsa_config --memory-limit 1000000000 --no-ts ``` -Then, create the visualisation as follows (`-t` is for plain text): +Then, create the visualisation in SVG format as follows: ```bash -tsalign show -i alignment.toml -n alignment-no-ts.toml -t +tsalign show -i alignment.toml -n alignment-no-ts.toml -s alignment.svg ``` - -Note that `-t` supports only simple cases of template switches, and may crash for more complicated cases. -For a more detailed and robust visualisation, use the parameter `-s visualisation.svg` to render the visualisation as SVG. Since SVGs are not always well supported, you can also use the switch `-p` to render the visualisation also as PNG. Note that the `-p` switch requires setting the `-s` parameter. ```bash -tsalign show -i alignment.toml -n alignment-no-ts.toml -ps visualisation.svg +tsalign show -i alignment.toml -n alignment-no-ts.toml -p -s visualisation.svg ``` -There are some switches to add more detail to the SVG and PNG visualisation. +There are additional switches and parameters to influence the visualisation. * `-a` adds arrows for the jumps of the alignments * `-c` renders more of the complements of the input sequences +* `-e` renders the heuristically computed uncertainties of a TSM with grey characters +* `-z X` renders only `x` bases of context around the TSMs ```bash -tsalign show -i alignment.toml -n alignment-no-ts.toml -ps visualisation.svg -ac +tsalign show -i alignment.toml -n alignment-no-ts.toml -ps visualisation.svg -ace -z 5 ``` ### Setting the alignment range @@ -156,5 +169,10 @@ ACACA|CCCAAC|GCGGG ACAAA|CGTGTC|GCGCG ``` -Now we can run `tsalign align -p input.delimited.fa --use-embedded-rq-ranges`. +Now we can run tsalign as follows: + +```bash +tsalign align -p input.delimited.fa --use-embedded-rq-ranges +``` + Now, tsalign will use much less resources, as it can ignore the non-matches before and after the focus region. From bd31816bd6ba6753ae0edc1cff44447d69927bf4 Mon Sep 17 00:00:00 2001 From: Sebastian Schmidt <61014855+sebschmi@users.noreply.github.com> Date: Tue, 19 May 2026 11:47:36 +0300 Subject: [PATCH 2/3] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 5545773d..1cb48a4c 100644 --- a/README.md +++ b/README.md @@ -41,11 +41,11 @@ If you ever want to update to a new release, simply run `cargo install tsalign` ### Python bindings -1. Install the python package manager [`pip`](https://pypi.org/project/pip/). +1. Install the Python package manager [`pip`](https://pypi.org/project/pip/). 2. Run `pip install tsalign`. -3. Refer to [the python bindings README](python_bindings/README.md) for more information. +3. Refer to [the Python bindings README](python_bindings/README.md) for more information. ### From Source (For Developers) From 12f85c2ee299941673be1564be29afb05e62b5cc Mon Sep 17 00:00:00 2001 From: Sebastian Schmidt <61014855+sebschmi@users.noreply.github.com> Date: Tue, 19 May 2026 11:49:00 +0300 Subject: [PATCH 3/3] Clarify genomic sequence alignment features Updated feature descriptions for clarity and consistency. --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1cb48a4c..d46f23ba 100644 --- a/README.md +++ b/README.md @@ -23,8 +23,8 @@ ## Features -* Align two genomic sequences while allowing for template switches. -* Visualise the alignment with template switch jumps. +* Align two genomic sequences while allowing for template switch mutations (TSMs). +* Visualise the alignment with template switching jumps. ## Installation @@ -133,7 +133,7 @@ There are additional switches and parameters to influence the visualisation. * `-a` adds arrows for the jumps of the alignments * `-c` renders more of the complements of the input sequences * `-e` renders the heuristically computed uncertainties of a TSM with grey characters -* `-z X` renders only `x` bases of context around the TSMs +* `-z X` renders only `X` bases of context around the TSMs ```bash tsalign show -i alignment.toml -n alignment-no-ts.toml -ps visualisation.svg -ace -z 5