Metadata-Version: 2.4
Name: synphage
Version: 0.2.8
Summary: Python library for plotting synteny diagram for phage and bacterial sequences.
Author-email: Virginie Grosboillot <vestalisvirginis@gmail.com>
License:                                  Apache License
                                   Version 2.0, January 2004
                                http://www.apache.org/licenses/
        
           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
        
           1. Definitions.
        
              "License" shall mean the terms and conditions for use, reproduction,
              and distribution as defined by Sections 1 through 9 of this document.
        
              "Licensor" shall mean the copyright owner or entity authorized by
              the copyright owner that is granting the License.
        
              "Legal Entity" shall mean the union of the acting entity and all
              other entities that control, are controlled by, or are under common
              control with that entity. For the purposes of this definition,
              "control" means (i) the power, direct or indirect, to cause the
              direction or management of such entity, whether by contract or
              otherwise, or (ii) ownership of fifty percent (50%) or more of the
              outstanding shares, or (iii) beneficial ownership of such entity.
        
              "You" (or "Your") shall mean an individual or Legal Entity
              exercising permissions granted by this License.
        
              "Source" form shall mean the preferred form for making modifications,
              including but not limited to software source code, documentation
              source, and configuration files.
        
              "Object" form shall mean any form resulting from mechanical
              transformation or translation of a Source form, including but
              not limited to compiled object code, generated documentation,
              and conversions to other media types.
        
              "Work" shall mean the work of authorship, whether in Source or
              Object form, made available under the License, as indicated by a
              copyright notice that is included in or attached to the work
              (an example is provided in the Appendix below).
        
              "Derivative Works" shall mean any work, whether in Source or Object
              form, that is based on (or derived from) the Work and for which the
              editorial revisions, annotations, elaborations, or other modifications
              represent, as a whole, an original work of authorship. For the purposes
              of this License, Derivative Works shall not include works that remain
              separable from, or merely link (or bind by name) to the interfaces of,
              the Work and Derivative Works thereof.
        
              "Contribution" shall mean any work of authorship, including
              the original version of the Work and any modifications or additions
              to that Work or Derivative Works thereof, that is intentionally
              submitted to Licensor for inclusion in the Work by the copyright owner
              or by an individual or Legal Entity authorized to submit on behalf of
              the copyright owner. For the purposes of this definition, "submitted"
              means any form of electronic, verbal, or written communication sent
              to the Licensor or its representatives, including but not limited to
              communication on electronic mailing lists, source code control systems,
              and issue tracking systems that are managed by, or on behalf of, the
              Licensor for the purpose of discussing and improving the Work, but
              excluding communication that is conspicuously marked or otherwise
              designated in writing by the copyright owner as "Not a Contribution."
        
              "Contributor" shall mean Licensor and any individual or Legal Entity
              on behalf of whom a Contribution has been received by Licensor and
              subsequently incorporated within the Work.
        
           2. Grant of Copyright License. Subject to the terms and conditions of
              this License, each Contributor hereby grants to You a perpetual,
              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
              copyright license to reproduce, prepare Derivative Works of,
              publicly display, publicly perform, sublicense, and distribute the
              Work and such Derivative Works in Source or Object form.
        
           3. Grant of Patent License. Subject to the terms and conditions of
              this License, each Contributor hereby grants to You a perpetual,
              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
              (except as stated in this section) patent license to make, have made,
              use, offer to sell, sell, import, and otherwise transfer the Work,
              where such license applies only to those patent claims licensable
              by such Contributor that are necessarily infringed by their
              Contribution(s) alone or by combination of their Contribution(s)
              with the Work to which such Contribution(s) was submitted. If You
              institute patent litigation against any entity (including a
              cross-claim or counterclaim in a lawsuit) alleging that the Work
              or a Contribution incorporated within the Work constitutes direct
              or contributory patent infringement, then any patent licenses
              granted to You under this License for that Work shall terminate
              as of the date such litigation is filed.
        
           4. Redistribution. You may reproduce and distribute copies of the
              Work or Derivative Works thereof in any medium, with or without
              modifications, and in Source or Object form, provided that You
              meet the following conditions:
        
              (a) You must give any other recipients of the Work or
                  Derivative Works a copy of this License; and
        
              (b) You must cause any modified files to carry prominent notices
                  stating that You changed the files; and
        
              (c) You must retain, in the Source form of any Derivative Works
                  that You distribute, all copyright, patent, trademark, and
                  attribution notices from the Source form of the Work,
                  excluding those notices that do not pertain to any part of
                  the Derivative Works; and
        
              (d) If the Work includes a "NOTICE" text file as part of its
                  distribution, then any Derivative Works that You distribute must
                  include a readable copy of the attribution notices contained
                  within such NOTICE file, excluding those notices that do not
                  pertain to any part of the Derivative Works, in at least one
                  of the following places: within a NOTICE text file distributed
                  as part of the Derivative Works; within the Source form or
                  documentation, if provided along with the Derivative Works; or,
                  within a display generated by the Derivative Works, if and
                  wherever such third-party notices normally appear. The contents
                  of the NOTICE file are for informational purposes only and
                  do not modify the License. You may add Your own attribution
                  notices within Derivative Works that You distribute, alongside
                  or as an addendum to the NOTICE text from the Work, provided
                  that such additional attribution notices cannot be construed
                  as modifying the License.
        
              You may add Your own copyright statement to Your modifications and
              may provide additional or different license terms and conditions
              for use, reproduction, or distribution of Your modifications, or
              for any such Derivative Works as a whole, provided Your use,
              reproduction, and distribution of the Work otherwise complies with
              the conditions stated in this License.
        
           5. Submission of Contributions. Unless You explicitly state otherwise,
              any Contribution intentionally submitted for inclusion in the Work
              by You to the Licensor shall be under the terms and conditions of
              this License, without any additional terms or conditions.
              Notwithstanding the above, nothing herein shall supersede or modify
              the terms of any separate license agreement you may have executed
              with Licensor regarding such Contributions.
        
           6. Trademarks. This License does not grant permission to use the trade
              names, trademarks, service marks, or product names of the Licensor,
              except as required for reasonable and customary use in describing the
              origin of the Work and reproducing the content of the NOTICE file.
        
           7. Disclaimer of Warranty. Unless required by applicable law or
              agreed to in writing, Licensor provides the Work (and each
              Contributor provides its Contributions) on an "AS IS" BASIS,
              WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
              implied, including, without limitation, any warranties or conditions
              of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
              PARTICULAR PURPOSE. You are solely responsible for determining the
              appropriateness of using or redistributing the Work and assume any
              risks associated with Your exercise of permissions under this License.
        
           8. Limitation of Liability. In no event and under no legal theory,
              whether in tort (including negligence), contract, or otherwise,
              unless required by applicable law (such as deliberate and grossly
              negligent acts) or agreed to in writing, shall any Contributor be
              liable to You for damages, including any direct, indirect, special,
              incidental, or consequential damages of any character arising as a
              result of this License or out of the use or inability to use the
              Work (including but not limited to damages for loss of goodwill,
              work stoppage, computer failure or malfunction, or any and all
              other commercial damages or losses), even if such Contributor
              has been advised of the possibility of such damages.
        
           9. Accepting Warranty or Additional Liability. While redistributing
              the Work or Derivative Works thereof, You may choose to offer,
              and charge a fee for, acceptance of support, warranty, indemnity,
              or other liability obligations and/or rights consistent with this
              License. However, in accepting such obligations, You may act only
              on Your own behalf and on Your sole responsibility, not on behalf
              of any other Contributor, and only if You agree to indemnify,
              defend, and hold each Contributor harmless for any liability
              incurred by, or claims asserted against, such Contributor by reason
              of your accepting any such warranty or additional liability.
        
           END OF TERMS AND CONDITIONS
        
           APPENDIX: How to apply the Apache License to your work.
        
              To apply the Apache License to your work, attach the following
              boilerplate notice, with the fields enclosed by brackets "[]"
              replaced with your own identifying information. (Don't include
              the brackets!)  The text should be enclosed in the appropriate
              comment syntax for the file format. We also recommend that a
              file or class name and description of purpose be included on the
              same "printed page" as the copyright notice for easier
              identification within third-party archives.
        
           Copyright [yyyy] [name of copyright owner]
        
           Licensed under the Apache License, Version 2.0 (the "License");
           you may not use this file except in compliance with the License.
           You may obtain a copy of the License at
        
               http://www.apache.org/licenses/LICENSE-2.0
        
           Unless required by applicable law or agreed to in writing, software
           distributed under the License is distributed on an "AS IS" BASIS,
           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
           See the License for the specific language governing permissions and
           limitations under the License.
        
Project-URL: Homepage, https://github.com/vestalisvirginis/synphage
Project-URL: Bug Tracker, https://github.com/vestalisvirginis/synphage
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: dagster==1.12.21
Requires-Dist: dagster-webserver==1.12.21
Requires-Dist: biopython==1.87
Requires-Dist: reportlab==4.2.2
Requires-Dist: rlPyCairo==0.4.0
Requires-Dist: cuallee==0.13.1
Requires-Dist: pandas==3.0.1
Requires-Dist: duckdb==1.1.0
Requires-Dist: polars==1.39.3
Requires-Dist: pyarrow==23.0.1
Requires-Dist: requests==2.33.0
Requires-Dist: pycairo==1.27.0
Requires-Dist: svgutils==0.3.4
Requires-Dist: cairosvg==2.9.0
Provides-Extra: dev
Requires-Dist: black==26.3.1; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: flake8; extra == "dev"
Requires-Dist: pre-commit>=4.5.1; extra == "dev"
Requires-Dist: radon>=6.0.1; extra == "dev"
Requires-Dist: ruff>=0.15.8; extra == "dev"
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Requires-Dist: coverage; extra == "test"
Provides-Extra: all
Requires-Dist: synphage[dev,test]; extra == "all"
Dynamic: license-file

[![PyPI version](https://badge.fury.io/py/synphage.svg)](https://badge.fury.io/py/synphage)
[![ci](https://github.com/vestalisvirginis/synphage/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/vestalisvirginis/synphage/actions/workflows/ci.yml)
[![codecov](https://codecov.io/github/vestalisvirginis/synphage/graph/badge.svg?token=HX32HRFS3V)](https://codecov.io/github/vestalisvirginis/synphage)
[![](https://img.shields.io/pypi/dm/synphage.svg?style=popout-square)](https://pypi.org/project/synphage/)
[![License](https://img.shields.io/github/license/vestalisvirginis/synphage.svg?style=popout-square)](https://opensource.org/licenses/Apache-2.0)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
<br>
<br>
<br>
<p align="center" style="padding: 80px 0 50px;">
  <img src="./logo/synphage_logo.png" alt="synphage logo" title="synphage logo" width="320" style="display: block; margin: 0 auto;" />
</p>
<br>
<br>

# synphage

Pipeline to create phage genome synteny graphics from genbank files

This library provides an intuitive tool for creating synteny graphics highlighting the conserved genes between multiple genome sequences.
This tool is primarily designed to work with phage genomes or other short sequences of interest, although it works with bacterial genomes as well.

Despite numerous synteny tools available on the market, this tool has been conceived because none of the available tools allows to visualise gene conservation in multiple sequences at one glance (as typically cross-links are drawn only between two consecutive sequences for a better readability).

As a result `synphage` was born.

In addition to show conserved genes across multiple sequences, the originality of this library stands in the fact that when working on the same set of genomes the initial blast and computation need to be run only once. Multiple graphics can then be generated from these data, comparing all the genomes or only a set of genomes from the analysed dataset. Moreover, the generated data is also available to the user as a table, where individual genes or groups of genes can easily be checked by name for conservation or uniqueness.


## Paper

`synphage` has been published in Bioinformatics Advances ([https://doi.org/10.1093/bioadv/vbae126](https://doi.org/10.1093/bioadv/vbae126)):

```
Virginie Grosboillot, Anna Dragoš, synphage: a pipeline for phage genome synteny graphics focused on gene conservation, Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae126, https://doi.org/10.1093/bioadv/vbae126
```

If you use `synphage` please cite this work.


## Install

`synphage` is available via [pip install](https://pypi.org/project/synphage/) or as [docker image](https://hub.docker.com/r/vestalisvirginis/synphage).
For more detailed instruction, consult [synphage installation guide](https://vestalisvirginis.github.io/synphage/installation/).

### Via pip
``` bash
pip install synphage
```
[See complete documention](https://vestalisvirginis.github.io/synphage/installation#/pip-install)

### Via docker
```bash
docker pull vestalisvirginis/synphage:<tag>
```
>[!NOTE]
>Replace `<tag>` with the [latest image tag](https://hub.docker.com/r/vestalisvirginis/synphage/tags).
[See complete documention](https://vestalisvirginis.github.io/synphage/installation#/docker-install)

### Additional dependencies

synphage relies on one non-python dependency that needs to be manually installed when synphage is installed with pip:
- [Blast+](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/) >= 2.12.0

Install `Blast+` using your package manager of choice, e.g. for linux ubuntu:
``` bash
apt update
apt install -y ncbi-blast+
```

or by downloading an [executables](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/) appropriate for your system. For help, check the complete [installation documentation](https://www.ncbi.nlm.nih.gov/books/NBK569861/).


## Usage

### Setup

synphage requires the user to specify the following environment variables:
- `INPUT_DIR` : to specify the path to the folder containing the user's `GenBank files`. If not set, this path will be defaulted to the temp folder. This path can also be modified at run time.
- `OUTPUT_DIR`: to specify the path to the folder where the data generated during the run will be stored. If not set, this path will be defaulted to the temp folder.
- `EMAIL` (optional): to connect to the NCBI database.
- `API_KEY` (optional): to connect to the NCBI database and download files.

>[!TIP]
>These variables can be set with a `.env` file located in your working directory (Dagster will automatically load them from the .env file when initialising the pipeline) or can be passed in the terminal before starting to run synphage:
>**.env**
>``` .env
>INPUT_DIR=path/to/my/data/
>OUTPUT_DIR=path/to/synphage/data
>EMAIL=user.email@email.com
>API_KEY=UserApiKey
>```
>**bash**
>``` bash
>export INPUT_DIR=<path_to_data_folder>
>export OUTPUT_DIR=<path_to_synphage_folder>
>export EMAIL=user.email@email.com
>export API_KEY=UserApiKey
>```

>[!NOTE]
>For docker users, the `INPUT_DIR` is defaulted to `/user_files` and `OUTPUT_DIR` is defaulted to `/data`.
> For more detailed explainations on using `synphage docker image`, check our [documentation](https://vestalisvirginis.github.io/synphage/installation/#run-synphage-container).


### Running Synphage

A step-by-step example, performed on a group of closely related *Lactococcus* phages is available in the [documentation](https://vestalisvirginis.github.io/synphage/phages/).

#### Starting Dagster

`synphage` uses [Dagster](https://dagster.io). In order to run synphage jobs, you need to start dagster first.

Set up the environment variable DAGSTER_HOME in order to keep a trace of your previous run (optional). For more information, see [Dagster documentation](https://docs.dagster.io/deployment/dagster-instance).

```bash
export DAGSTER_HOME=<dagster_home_directory>

dagster dev -h 0.0.0.0 -p 3000 -m synphage
```

For docker users:
```bash
docker run -p 3000 vestalisvirginis/synphage:<tag>
```
For more information and options, check [running synphage container](https://vestalisvirginis.github.io/synphage/installation/#run-synphage-container).

#### Running the jobs

synphage pipeline is composed of `four steps` that need to be run `sequencially`.
[See complete documention](https://vestalisvirginis.github.io/synphage/pipeline)

##### Step 1: Loading the data into the pipeline
Data is loaded into the pipeline from the `input_folder` set by the user `and/or` `downloaded` from the NCBI.
- `step_1a_get_user_data` : load user's data
- `step_1b_download` : download data from the NCBI

> [!IMPORTANT]
> - Only one of the jobs is required to successfully run step 1.
> - Configuration is required for `step_1b_download` job: `search_key`, that receives the keywords for querying the NCBI database.

###### Query config options :
Field Name | Description | Default Value
 ------- | ----------- | ----
`search_key` | Keyword(s) for NCBI query | Myoalterovirus


> [!TIP]
> Both jobs can be run if the user needs both, local and downloaded files.

##### Step 2: Data validation
Completeness of the data is validated at this step.
- `step_2_make_validation` : perform checks and transformations on the dataset that are required for downstream processing

> [!IMPORTANT]
> This step is required and cannot be skipped.

##### Step 3: Blasting the data
The blast is performed at this step of the pipeline and three different `options` are available:
- `step_3a_make_blastn` : run a Nucleotide BLAST on the dataset
- `step_3b_make_blastp` : run a Protein BLAST on the dataset
- `step_3c_make_all_blast` : run both, Nucleotide and Protein BLAST simultaneously

> [!IMPORTANT]
> Only one of the above jobs is required to successfully run step 3.

> [!TIP]
> Both `step_3a_make_blastn` and `step_3b_make_blastp` jobs can be run sequencially, mainly in the case where the user decide to run the second job based on the results obtained for the first one.


##### Step 4: Synteny plot
The graph is created during this last step. The step 4 can be run multiple times with different configurations and different sets of data, as long as the data have been processed once through steps 1, 2 and 3.
- `step_4_make_plot` : use data generated at step 3 and the genbank files to plot the synteny diagram

> [!IMPORTANT]
> Configuration is require for `step_4_make_plot` job: `graph_type`, that receives either `blastn` or `blastp` as value for specifying what dataset to use for the plot. Default value is set to `blastn`. For more information about the configuration at step 4, check the [documentation](https://vestalisvirginis.github.io/synphage/configurations/).

> [!TIP]
> Different synteny plots can be generated from the same set of genomes. In this case the three first steps only need to be run once and the fourth step, `step_4_make_plot`, can be triggered separately for each graphs.
> For modifying the sequences to be plotted (selected sequences, order, orientation), the sequences.csv file generated at step3 can be modify and saved under a different name. This new `.csv` can be passed in the job configuration `sequence_file`.
>
> *sequences.csv*
> ``` txt
> genome_1.gb,0
> genome_2.gb,1
> genome_3.gb,0
> ```

###### Plotting config options

The appearance of the plot can be modified through the configuration.

Field Name | Description | Default Value
 ------- | ----------- | ----
`title` | Generated plot file title | synteny_plot
`graph_type` | Type of dataset to use for the plot | blastn
`colours` | Gene identity colour bar | ["#fde725", "#90d743", "#35b779", "#21918c", "#31688e", "#443983", "#440154"]
`gradient` | Nucleotide identity colour bar | #B22222
`graph_shape` | Linear or circular representation | linear
`graph_pagesize` | Output document format | A4
`graph_fragments` | Number of fragments | 1
`graph_start` | Sequence start | 1
`graph_end` | Sequence end | length of the longest genome


## Output

synphage's output consists of four to six main parquet files (depending if blastn and blastp were both executed) and the synteny graphic. However all the data generated by the synphage pipeline are made available in your data directory.

### Generated data architecture

```
.
├── <path_to_synphage_folder>/
│   ├── download/
│   ├── fs/
│   ├── genbank/
│   ├── gene_identity/
│   │   ├── fasta_n/
│   │   ├── blastn_database/
│   │   └── blastn/
│   ├── protein_identity/
│   │   ├── fasta_p/
│   │   ├── blastp_database/
│   │   └── blastp/
│   ├── tables/
│   │   ├── genbank_db.parquet
│   │   ├── processed_genbank_df.parquet
│   │   ├── blastn_summary.parquet
│   │   ├── blastp_summary.parquet
│   │   ├── gene_uniqueness.parquet
│   │   └── protein_uniqueness.parquet
│   ├── sequences.csv
│   └── synteny/
│      ├── colour_table.parquet
│      ├── synteny_graph.png
│      └── synteny_graph.svg
└── ...
```


### Tables

The `tables` folder contains the four to six main parquet files generated by the pipeline.
1. `genbank_db.parquet` : original data parsed from the GenBank files.
2. `processed_genbank_df.parquet` : data processed during the validation step. It contains two additional columns:
   - `gb_type` : specifying what type of data is used as unique identifier of the coding elements
   - `key`: unique identifier based on the columns: `filename`, `id` and `locus_tag`.
3. `blastn_summary.parquet` : data parsed from the `blastn` output json files. It contains the collection of the best match for each sequence against each genomes. The percentage of identity between two sequences are then used for calculating the plot cross-links between the sequences.
4. `blastp_summary.parquet` : data parsed from the `blastp` output json files. It contains the collection of the best match for each sequence against each genomes. The percentage of identity between two sequences are then used for calculating the plot cross-links between the sequences.
5. `gene_uniqueness.parquet` : combines both `processed_genbank_df.parquet` and `blastn_summary.parquet` in a single parquet file, allowing the user to quickly know how many matches their sequence(s) of interest has/have retrieved. These data are then used to compute the colour code used for the synteny plot. The result of the computation is recorded in the `colour_table.parquet`. This file is over-written between each `plot` run.
6. `protein_uniqueness.parquet` : combines both `processed_genbank_df.parquet` and `blastp_summary.parquet` in a single parquet file, allowing the user to quickly know how many matches their sequence(s) of interest has/have retrieved. These data are then used to compute the colour code used for the synteny plot. The result of the computation is recorded in the `colour_table.parquet`. This file is over-written between each `plot` run.


### Synteny plot

The `synteny plot` is generated as `.svg file` and `.png file`, and contains the sequences indicated in the `sequences.csv` file. The genes are colour-coded according to their abundance (percentage) among the plotted sequences. The cross-links between each consecutive sequence indicates the percentage of similarities between those two sequences.


## Documentation

Visit [https://vestalisvirginis.github.io/synphage/](https://vestalisvirginis.github.io/synphage/) for complete [installation instruction](https://vestalisvirginis.github.io/synphage/installation/), [guidelines to navigate the pipeline](https://vestalisvirginis.github.io/synphage/pipeline/) and [step-by-step example](https://vestalisvirginis.github.io/synphage/phages/).


## Support

**Where to ask for help?**

Open a [discussion](https://github.com/vestalisvirginis/synphage/discussions).


## Roadmap

- ~~[x] create config options for the plot at run time~~
- ~~[x] integrate the NCBI search~~
- ~~[x] implement blastp~~
- [ ] create possibility to add ref sequence with special colour coding
- [ ] create interactive plot
- [ ] comparison based on structure
- [ ] Help us in a discussion?


## Status

`[2024-07-20]`   ✨ __New features!__
- `Checks` : to validate the quality of the data
- `Blastp` is finally implemented


`[2024-01-11]`   ✨ __New feature!__   to simplify the addition of new sequences into the genbank folder
 - `download` : download genomes to be analysed from the NCBI database


## Contributing

We accept different types of contributions, including some that don't require you to write a single line of code. For detailed instructions on how to get started with our project, see [CONTRIBUTING](CONTRIBUTING.md) file.


## Authors
- [vestalisvirginis](https://github.com/vestalisvirginis) / Virginie Grosboillot / 🇫🇷


<!-- ## Contributors
<a href="https://github.com/vestalisvirginis/synphage/graphs/contributors">
  <img src="https://contrib.rocks/image?repo=vestalisvirginis/synphage" />
</a> -->

## License
Apache License 2.0
Free for commercial use, modification, distribution, patent use, private use.
Just preserve the copyright and license.


> Made with ❤️ in Ljubljana 🇸🇮
