cool-seq-tool 0.3.0.dev0__py3-none-any.whl → 0.4.0.dev0__py3-none-any.whl

cool_seq_tool-0.3.0.dev0.dist-info/METADATA

@@ -1,187 +0,0 @@
-Metadata-Version: 2.1
-Name: cool-seq-tool
-Version: 0.3.0.dev0
-Summary: Common Operations On Lots-of Sequences Tool.
-Home-page: https://github.com/GenomicMedLab/cool-seq-tool
-Author: Wagner Lab, Nationwide Childrens Hospital
-License: MIT
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: asyncpg
-Requires-Dist: aiofiles
-Requires-Dist: boto3
-Requires-Dist: pyliftover
-Requires-Dist: polars
-Requires-Dist: hgvs
-Requires-Dist: biocommons.seqrepo
-Requires-Dist: pydantic ~=2.4.2
-Requires-Dist: uvicorn
-Requires-Dist: fastapi
-Requires-Dist: ga4gh.vrs
-Provides-Extra: dev
-Requires-Dist: pre-commit ; extra == 'dev'
-Requires-Dist: ipython ; extra == 'dev'
-Requires-Dist: ipykernel ; extra == 'dev'
-Requires-Dist: psycopg2-binary ; extra == 'dev'
-Requires-Dist: ruff ; extra == 'dev'
-Requires-Dist: black ; extra == 'dev'
-Provides-Extra: tests
-Requires-Dist: pytest ; extra == 'tests'
-Requires-Dist: pytest-cov ; extra == 'tests'
-Requires-Dist: pytest-asyncio ==0.18.3 ; extra == 'tests'
-Requires-Dist: mock ; extra == 'tests'
-
-# **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:uta@localhost:5433/uta/uta_20210129`).
-
-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:password@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
-```
-
-#### 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/).
-
-#### transcript_mapping.tsv
-`cool-seq-tool` is packaged with transcript mapping data acquired from [Ensembl BioMart](http://www.ensembl.org/biomart/martview). If the environment variable `TRANSCRIPT_MAPPINGS_PATH` is not set, `cool-seq-tool` will use the built-in file. When `TRANSCRIPT_MAPPINGS_PATH` is set, `cool_seq_tool` will look at this path and expect to find the transcript mapping TSV file.
-
-To acquire this data manually from the [BioMart](https://www.ensembl.org/biomart/martview), select the `Human Genes (GRCh38.p13)` dataset and choose the following attributes:
-
-* 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
-
-![image](biomart.png)
-
-## Starting the UTA Tools Service Locally
-
-To start the service, run the following:
-
-```commandline
-uvicorn cool_seq_tool.api: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 [Ruff](https://github.com/astral-sh/ruff) and [Black](https://github.com/psf/black), and should be 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
-```

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