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cool-seq-tool-0.1.9
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مشاهده بیشترتوضیحات
Common Operations On Lots-of Sequences Tool.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cool-seq-tool-0.1.9 |
| نام | cool-seq-tool |
| نسخه کتابخانه | 0.1.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Wagner Lab, Nationwide Childrens Hospital |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | https://github.com/GenomicMedLab/cool-seq-tool |
| آدرس اینترنتی | https://pypi.org/project/cool-seq-tool/ |
| مجوز | MIT |
# **C**ommon **O**perations **O**n **L**ots-of **Seq**uences Tool
The **cool-seq-tool** provides:
- Transcript alignment data from the [UTA](https://github.com/biocommons/uta) database
- Fast access to sequence data using [SeqRepo](https://github.com/biocommons/biocommons.seqrepo)
- Liftover between assemblies (GRCh38 <--> GRCh37) from [PyLiftover](https://github.com/konstantint/pyliftover)
- Lifting over to preferred [MANE](https://www.ncbi.nlm.nih.gov/refseq/MANE/) compatible transcript. See [here](docs/TranscriptSelectionPriority.md) for more information.
## Installation
### pip
```commandline
pip install cool-seq-tool[dev,tests]
```
### Development
Clone the repo:
```commandline
git clone https://github.com/GenomicMedLab/cool-seq-tool
cd cool_seq_tool
```
[Install Pipenv](https://pipenv-fork.readthedocs.io/en/latest/#install-pipenv-today) if necessary.
Install backend dependencies and enter Pipenv environment:
```commandline
pipenv shell
pipenv update
pipenv install --dev
```
### UTA Database Installation
`cool-seq-tool` uses intalls local UTA database. For other ways to install, visit [biocommons.uta](https://github.com/biocommons/uta).
#### Local Installation
_The following commands will likely need modification appropriate for the installation environment._
1. Install [PostgreSQL](https://www.postgresql.org/)
2. Create user and database.
```
$ createuser -U postgres uta_admin
$ createuser -U postgres anonymous
$ createdb -U postgres -O uta_admin uta
```
3. To install locally, from the _cool_seq_tool/data_ directory:
```
export UTA_VERSION=uta_20210129.pgd.gz
curl -O http://dl.biocommons.org/uta/$UTA_VERSION
gzip -cdq ${UTA_VERSION} | grep -v "^REFRESH MATERIALIZED VIEW" | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5433
```
##### UTA Installation Issues
If you have trouble installing UTA, you can visit [these two READMEs](https://github.com/ga4gh/vrs-python/tree/main/docs/setup_help).
#### Connecting to the database
To connect to the UTA database, you can use the default url (`postgresql://uta_admin@localhost:5433/uta/uta_20210129`). If you use the default url, you must either set the password using environment variable `UTA_PASSWORD` or setting the parameter `db_pwd` in the UTA class.
If you do not wish to use the default, you must set the environment variable `UTA_DB_URL` which has the format of `driver://user:pass@host:port/database/schema`.
### Data Downloads
#### SeqRepo
`cool-seq-tool` relies on [seqrepo](https://github.com/biocommons/biocommons.seqrepo), which you must download yourself.
Use the `SEQREPO_ROOT_DIR` environment variable to set the path of an already existing SeqRepo directory. The default is `/usr/local/share/seqrepo/latest`.
From the _root_ directory:
```
pip install seqrepo
sudo mkdir /usr/local/share/seqrepo
sudo chown $USER /usr/local/share/seqrepo
seqrepo pull -i 2021-01-29 # Replace with latest version using `seqrepo list-remote-instances` if outdated
```
If you get an error similar to the one below:
```
PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2021-01-29._fkuefgd' -> '/usr/local/share/seqrepo/2021-01-29'
```
You will want to do the following:\
(*Might not be ._fkuefgd, so replace with your error message path*)
```console
sudo mv /usr/local/share/seqrepo/2021-01-29._fkuefgd /usr/local/share/seqrepo/2021-01-29
exit
```
#### transcript_mappings.tsv
`cool-seq-tool` uses [Ensembl BioMart](http://www.ensembl.org/biomart/martview) to retrieve `cool_seq_tool/data/transcript_mappings.tsv`. We currently use `Human Genes (GRCh38.p13)` for the dataset and the following attributes we use are: Gene stable ID, Gene stable ID version, Transcript stable ID, Transcript stable ID version, Protein stable ID, Protein stable ID version, RefSeq match transcript (MANE Select), Gene name.
Use the `TRANSCRIPT_MAPPINGS_PATH` environment variable to set the path of an already existing `transcript_mappings.tsv`. The default is `cool_seq_tool/data/transcript_mapping.tsv`.
#### LRG_RefSeqGene
`cool-seq-tool` fetches the latest version of `LRG_RefSeqGene` if the environment variable `LRG_REFSEQGENE_PATH` is not set. When `LRG_REFSEQGENE_PATH` is set, `cool-seq-tool` will look at this path and expect the LRG_RefSeqGene file. This file is found can be found [here](https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene).
#### MANE Summary Data
`cool-seq-tool` fetches the latest version of `MANE.GRCh38.*.summary.txt.gz` if the environment variable `MANE_SUMMARY_PATH` is not set. When `MANE_SUMMARY_PATH` is set, `cool-seq-tool` will look at this path and expect the MANE Summary Data file. This file is found can be found [here](https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/current/).
## Starting the UTA Tools Service Locally
To start the service, run the following:
```commandline
uvicorn cool_seq_tool.main:app --reload
```
Next, view the FastAPI on your local machine: http://127.0.0.1:8000/cool_seq_tool
## Init coding style tests
Code style is managed by [flake8](https://github.com/PyCQA/flake8) and checked prior to commit.
We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.
This ensures:
* Check code style
* Check for added large files
* Detect AWS Credentials
* Detect Private Key
Before first commit run:
```
pre-commit install
```
## Testing
From the _root_ directory of the repository:
```
pytest
```
نیازمندی
| مقدار | نام |
|---|---|
| - | aiofiles |
| - | asyncpg |
| - | biocommons.seqrepo |
| - | boto3 |
| - | fastapi |
| - | ga4gh.vrs |
| !=0.2.0,!=0.2.1,!=0.2.2,!=0.2.3,!=0.2.4,!=0.2.5,!=0.2.6,!=0.2.7,!=0.2.8,>=0.1.34 | gene-normalizer |
| - | hgvs |
| - | pandas |
| - | pydantic |
| - | pyliftover |
| - | uvicorn |
| - | flake8 |
| - | flake8-annotations |
| - | flake8-docstrings |
| - | flake8-import-order |
| - | flake8-quotes |
| - | ipykernel |
| - | ipython |
| - | pre-commit |
| - | psycopg2-binary |
| - | mock |
| - | pytest |
| ==0.18.3 | pytest-asyncio |
| - | pytest-cov |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl cool-seq-tool-0.1.9:
pip install cool-seq-tool-0.1.9.whl
نصب پکیج tar.gz cool-seq-tool-0.1.9:
pip install cool-seq-tool-0.1.9.tar.gz