https://github.com/brsynth/rpbasicdesign
Convert rpSBML file to SBOL + CSV files ready to be used by DNA-Bot.
https://github.com/brsynth/rpbasicdesign
dna-bot synbio synthetic-biology
Last synced: 4 months ago
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Convert rpSBML file to SBOL + CSV files ready to be used by DNA-Bot.
- Host: GitHub
- URL: https://github.com/brsynth/rpbasicdesign
- Owner: brsynth
- License: mit
- Created: 2020-10-23T09:03:10.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-05-17T09:45:08.000Z (about 3 years ago)
- Last Synced: 2025-10-21T19:40:04.687Z (8 months ago)
- Topics: dna-bot, synbio, synthetic-biology
- Language: Python
- Homepage:
- Size: 338 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.txt
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README
# rpbasicdesign
[](https://anaconda.org/conda-forge/rpbasicdesign)
[](https://anaconda.org/conda-forge/rpbasicdesign)
**A command-line tool to convert rpSBML files into SBOL and CSV files ready-to-be used with DNA-Bot.**
**rpbasicdesign** extracts enzyme IDs from rpSBML files -- produced by the RP suite available in the
[SynBioCAD Galaxy platform](https://galaxy-synbiocad.org) -- to generate genetic constructs compliant with
the [BASIC](https://doi.org/10.1021/sb500356d) assembly approach. CSV files produced are ready to be used with
[DNA-Bot](https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT) to generate instructions for automated build of the
genetic constructs using [OpenTrons](https://opentrons.com/) liquid handling robots.
## Installation
```sh
conda install -c brsynth -c conda-forge rpbasicdesign
```
## Usage
Simple call:
```sh
conda activate
python -m rpbasicdesign.cli --rpsbml_file tests/input/muconate_example.xml
```
Output folders for dnabot-ready files and SBOL export can be set using `o_dnabot_dir` and `o_sbol_dir` options:
```sh
python -m rpbasicdesign.cli \
--rpsbml_file tests/input/muconate_example.xml \
--o_dnabot_dir out/dnabot_input \
--o_sbol_dir out/sbol_export
```
The number of constructs to design is tuned using `sample_size`:
```sh
python -m rpbasicdesign.cli \
--rpsbml_file tests/input/muconate_example.xml \
--sample_size 5
```
The complete list options is provided the embedded help, which can be printed using the `--help` or `-h` keywords:
```
python -m rpbasicdesign.cli -h
usage: python -m rpbasicdesign.cli [-h]
--rpsbml_file RPSBML_FILE
[--parts_files PARTS_FILES [PARTS_FILES ...]]
[--lms_id LMS_ID]
[--lmp_id LMP_ID]
[--backbone_id BACKBONE_ID]
[--sample_size SAMPLE_SIZE]
[--cds_permutation CDS_PERMUTATION]
[--max_enz_per_rxn MAX_ENZ_PER_RXN]
[--o_dnabot_dir O_DNABOT_DIR]
[--o_sbol_dir O_SBOL_DIR]
Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly chosen from a default list. CDSs, in other words gene variants,
of enzymes are randomly chosen from amongst the UniProt IDs extracted. Constructs generated can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL files.
optional arguments:
-h, --help show this help message and exit
--rpsbml_file RPSBML_FILE
rpSBML file from which enzymes UniProt IDs will be collected.
--parts_files PARTS_FILES [PARTS_FILES ...]
List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv]
--lms_id LMS_ID part ID to be used as the LMS methylated linker. Default: LMS
--lmp_id LMP_ID part ID to be used as the LMP methylated linker. Default: LMP
--backbone_id BACKBONE_ID
part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1
--sample_size SAMPLE_SIZE
Number of construct to generate.Default: 88
--cds_permutation CDS_PERMUTATION
Whether all combinations of CDS permutation should be built Default: true
--max_enz_per_rxn MAX_ENZ_PER_RXN
Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept.
--max_gene_per_construct MAX_GENE_PER_CONSTRUCT
Maximum number of genes per construct. If more genes are required, i.e. more reactions are described in the inputet SBML file, then the execution will failed.
--o_dnabot_dir O_DNABOT_DIR
Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in
--o_sbol_dir O_SBOL_DIR
Output folder to write SBOL depictions of constructs. Existing files will be overwritten. Default: not output.
```
## Lycopene example
If one wishes to only use a subset of BASIC parts, the way to go is to
provide a restricted list of parts with the `--parts_file` option.
The command below generates up to 88 constructs for the lycopene producing
pathway (CrtEBI pathway) defined in `examples/lycopene_CrtEBI_from_selenzy.xml.xml`, using the parts
described in `examples/parts_for_lycopene.csv`. Output files will be written
in `examples/lycopene_sbol` folder for SBOL files and `examples/lycopene_dnabot`
for DNA-Bot. At the end 88 constructs should be outputted.
```bash
python -m rpbasicdesign.cli --rpsbml_file examples/lycopene_CrtEBI_from_selenzy.xml --sample_size 88 --parts_files examples/parts_for_lycopene.csv --o_sbol_dir examples/lycopene_sbol_crtEBI --o_dnabot_dir examples/lycopene_dnabot_crtEBI --max_enz_per_rxn 1
```
## Inputs
This section documents input files required / optional, their purpose, and how information should be structured.
### rpSBML file [required]
SBML with retropath-like annotations. UnitProt IDs of enzyme are expected to be listed here. More information of rpSBML file at [https://github.com/brsynth/rptools](https://github.com/brsynth/rptools). Some examples or rpSBML files are provided in `tests/input`.
### Parts files [optional]
These are CSV files listing the linker IDs available for the constructs (BASIC linkers), as well as the user parts (backbone, promoters, ...). The format should be comma separated on 4 columns with header. Example below:
```
id,type,sequence,comment
L1,neutral linker,,
L2,neutral linker,,
L3,neutral linker,,
```
By default, the `rpbasicdesign/data/biolegio_parts.csv` file is used which corresponds to the BioLegio commercial plate ([link](https://www.biolegio.com/products-services/basic/)). A second predefined file corresponding to older version of the BioLegio plate is also described in `rpbasicdesign/data/legacy_parts.csv`.
For linkers, the `type` annotation should be one of `neutral linker`, `methylated linker`, `peptide fusion linker` or `RBS linker`. For user parts, `type` should be one of `backbone` or `constitutive promoter`. Other type will raise a warning and will be omited. By default, [biolegio_parts.csv](rpbasicdesign/data/biolegio_parts.csv) and [user_parts.csv](rpbasicdesign/data/user_parts.csv) are used.
Use the `parts_files` arguments to override.
**Important**:
- IDs should match the linker naming conventions (see below).
- IDs should match the IDs used in the plate file inputed to dnabot. As example -- but also ready to be used -- the [biolegio_plate.csv](rpbasicdesign/data/biolegio_plate.csv) is a valid input files for dnabot, with consistent IDs between `biolegio_parts.csv` and `biolegio_plate.csv`.
## For developers
### Installation
```sh
git clone https://github.com/brsynth/rpbasicdesign.git
cd rpbasicdesign
conda env create -f environment.yaml -n
conda develop -n .
```
### Tests
```sh
conda activate
python -m pytest -v --cov=rpbasicdesign --cov-report html
```
## Constraints and limitations
The BASIC linker set is a major piece of the BASIC assembly method. For a detailed explanation of the BASIS approach,
see Storch et. al., ACS Synth. Biol., 2015 (doi: [10.1021/sb500356d](https://doi.org/10.1021/sb500356d)).
### Polycistronic constructs
Only polycistronic constructs are enabled at the moment.
### Predefined set of linkers
By default, the set of linkers used is the one presented available in from the commercial plate from BioLegio.
If one wants to use its own set of linkers, the user is advised to do it carefully and to look for more information.
### Linker naming conventions
Due to DNA-Bot implementation:
- RBS linkers should start with the `Un` suffix, where `n` could be any alphanumeric character.
- Any linkers should have its two half linkers ending with the `-P` and `-S` suffixes listed in the "plate" file, ie in the file that provides the well locations containing the DNA fragment. See the BASIC approach paper, and especially the supplementary files for more information.
### Controlled vocabulary for parts file
Parts and linkers provided in the `*_parts.csv` files have to match on the following type:
- `neutral linker`
- `methylated linker`
- `RBS linker`
- `peptide fusion linker`
- `backbone`
- `constitutive promoter`
### Providing CDSs
As of today, CDS are obtained only by parsing rpSBML files.
### Custom linkers
For advanced users wishing to play with custom linkers:
- Linkers and parts can be provided using a custom file with the `--parts_files` argument.
- Linkers described `user_parts.csv` are not considered.
- RBS linker IDs have to be in the form `AAA-BBB` with `AAA` being the linker suffix ID.
- Linker prefixes and suffixes coordinates on the plate have to be listed in `[biolegio|legacy]_plate.csv`.
### Maximum number of CDSs per construct
The maximum number of genes in a construct limited to 3 with the default `biolegio_plate.csv` RBS library, because
there is only 3 different RBS suffix in the commercial BioLegio library. Anyway, if needed, this max number of genes
can be relaxed and increased using the `--max_gene_per_construct` parameter.
## TODO
- Better handle logs and add `verbose` option
## References
- Galaxy-SynBioCAD: https://doi.org/10.1101/2020.06.14.145730
- DNA-Bot: https://doi.org/10.1093/synbio/ysaa010
- BASIC assembly method: https://doi.org/10.1021/sb500356d