cool-seq-tool 0.3.0.dev1__py3-none-any.whl → 0.4.0.dev1__py3-none-any.whl

cool_seq_tool/utils.py

@@ -1,7 +1,7 @@
-"""Module for common utilities used throughout the app"""
+"""Provide a small set of general helper functions."""
 import logging
 from datetime import datetime
-from typing import Optional, Tuple
+from typing import Tuple
 
 from cool_seq_tool.schemas import ResidueMode, ServiceMeta
 from cool_seq_tool.version import __version__
@@ -10,38 +10,36 @@ logger = logging.getLogger(__name__)
 
 
 def get_inter_residue_pos(
-    start_pos: int, residue_mode: ResidueMode, end_pos: Optional[int] = None
-) -> Tuple[Optional[Tuple[int, int]], Optional[str]]:
-    """Return inter-residue position
+    start_pos: int, end_pos: int, residue_mode: ResidueMode
+) -> Tuple[int, int]:
+    """Return equivalent inter-residue position.
+
+    Generally, we prefer to work with inter-residue coordinates where possible. Our
+    rationale is detailed in an appendix to the
+    `VRS docs <https://vrs.ga4gh.org/en/stable/appendices/design_decisions.html#inter-residue-coordinates>`_.
+    This function is used internally to shift user-provided coordinates accordingly.
+
+    >>> from cool_seq_tool.utils import get_inter_residue_pos
+    >>> from cool_seq_tool.schemas import ResidueMode
+    >>> get_inter_residue_pos(10, ResidueMode.RESIDUE)
+    ((9, 9), None)
 
     :param start_pos: Start position
+    :param end_pos: End position
     :param residue_mode: Residue mode for `start_pos` and `end_pos`
-    :param end_pos: End position. If `None` assumes both `start` and `end` have same
-        values.
-    :return: Inter-residue coordinates, warning
+    :return: Inter-residue coordinates
     """
     if residue_mode == ResidueMode.RESIDUE:
         start_pos -= 1
-        if end_pos is None:
-            end_pos = start_pos
-        else:
-            end_pos -= 1
-    elif residue_mode == ResidueMode.INTER_RESIDUE:
-        if end_pos is None:
-            end_pos = start_pos
-    else:
-        msg = (
-            f"residue_mode must be either `residue` or `inter-residue`,"
-            f" not `{residue_mode}`"
-        )
-        logger.warning(msg)
-        return None, msg
-    return (start_pos, end_pos), None
+    elif residue_mode == ResidueMode.ZERO:
+        end_pos += 1
+    return start_pos, end_pos
 
 
 @staticmethod
 def service_meta() -> ServiceMeta:
-    """Return ServiceMeta for cool_seq_tool
+    """Return description of request and service, including parameters like software
+    version for reproducibility.
 
     :return: ServiceMeta object
     """

cool_seq_tool/version.py

@@ -1,2 +1,2 @@
 """Define package version."""
-__version__ = "0.3.0-dev1"
+__version__ = "0.4.0-dev1"

{cool_seq_tool-0.3.0.dev1.dist-info → cool_seq_tool-0.4.0.dev1.dist-info}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 VICC
+Copyright (c) 2021-2023 Wagner Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

cool_seq_tool-0.4.0.dev1.dist-info/METADATA

@@ -0,0 +1,130 @@
+Metadata-Version: 2.1
+Name: cool_seq_tool
+Version: 0.4.0.dev1
+Summary: Common Operation on Lots of Sequences Tool
+Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
+License: MIT License
+        
+        Copyright (c) 2021-2023 Wagner Lab
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/genomicmedlab/cool-seq-tool
+Project-URL: Documentation, https://coolseqtool.readthedocs.io/en/latest/index.html
+Project-URL: Changelog, https://github.com/genomicmedlab/cool-seq-tool/releases
+Project-URL: Source, https://github.com/genomicmedlab/cool-seq-tool
+Project-URL: Bug Tracker, https://github.com/genomicmedlab/cool-seq-tool/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Framework :: FastAPI
+Classifier: Framework :: Pydantic
+Classifier: Framework :: Pydantic :: 2
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+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.*
+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'
+Provides-Extra: docs
+Requires-Dist: sphinx ==6.1.3 ; extra == 'docs'
+Requires-Dist: sphinx-autodoc-typehints ==1.22.0 ; extra == 'docs'
+Requires-Dist: sphinx-autobuild ==2021.3.14 ; extra == 'docs'
+Requires-Dist: sphinx-copybutton ==0.5.2 ; extra == 'docs'
+Requires-Dist: sphinxext-opengraph ==0.8.2 ; extra == 'docs'
+Requires-Dist: furo ==2023.3.27 ; extra == 'docs'
+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'
+
+<h1 align="center">
+CoolSeqTool
+</h1>
+
+**[Documentation](https://coolseqtool.readthedocs.io/en/latest/)** · [Installation](https://coolseqtool.readthedocs.io/en/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/en/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/en/latest/reference/index.html)
+
+## Overview
+
+<!-- description -->
+The **CoolSeqTool** provides:
+
+ - A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and the [Universal Transcript Archive](https://github.com/biocommons/uta)
+ - Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
+ - Mapping tools that combine the above to support translation between references sequences, annotation layers, and MANE transcripts
+<!-- /description -->
+
+---
+
+## Install
+
+CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
+
+```shell
+python3 -m pip install cool-seq-tool
+```
+
+See the [installation instructions](https://coolseqtool.readthedocs.io/en/latest/install.html) in the documentation for a description of dependency setup requirements.
+
+---
+
+## Usage
+
+All CoolSeqTool resources can be initialized by way of a top-level class instance:
+
+```pycon
+>>> from cool_seq_tool.app import CoolSeqTool
+>>> cst = CoolSeqTool()
+>>> result = await cst.mane_transcript.get_mane_transcript(
+...     "NP_004324.2",
+...     599,
+...     AnnotationLayer.PROTEIN,
+...     residue_mode=ResidueMode.INTER_RESIDUE,
+... )
+>>> result.gene, result.refseq, result.status
+('EGFR', 'NM_005228.5', <TranscriptPriority.MANE_SELECT: 'mane_select'>)
+```
+
+---
+
+## Feedback and contributing
+
+We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/en/latest/contributing.html) contains guidance for submitting feedback and contributing new code.

cool_seq_tool-0.4.0.dev1.dist-info/RECORD

@@ -0,0 +1,29 @@
+cool_seq_tool/__init__.py,sha256=eBycAZIAJBCf51xQLQYHzvUep1i21LMrzBdRLqfe-Fc,352
+cool_seq_tool/api.py,sha256=3Pc0j0pHMZ_3skTkjDlQpcu_MM6kyNPmBrwm_LrH-rw,1234
+cool_seq_tool/app.py,sha256=3r2hlajW6xjf3u_Uf9WlqMfBEK-LnB74sG2UpJlj2bY,3757
+cool_seq_tool/paths.py,sha256=7EA21Vmf9hvct0z_V4oK0WTWOA2FKY2Tavh4nAUXunk,889
+cool_seq_tool/schemas.py,sha256=miroNMyC1i6I4OuMZwJ0WQq3dBhtvuYPsMevahWQI5k,15697
+cool_seq_tool/utils.py,sha256=EkDFKh6allYu_BaODuosALECm8z64JiovXC8yHd2kHY,1583
+cool_seq_tool/version.py,sha256=00BKrYQ_DDUCwzibwzXpM7JCXVp-i5tZlTE4r8vs2eA,57
+cool_seq_tool/data/__init__.py,sha256=EAk0f_xeq1JAkRosLMiWWhEXku6lYfMZ63HR_6QxSqs,77
+cool_seq_tool/data/data_downloads.py,sha256=Jlt9YYxkJdUuDwXmuRheZ7D4deArlYLQUNsr4CQwYNE,3747
+cool_seq_tool/data/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
+cool_seq_tool/handlers/__init__.py,sha256=xDQ84N4ImrUBKwGmrg64yGUMh0ArW-DwjJuTkKrIJL4,77
+cool_seq_tool/handlers/seqrepo_access.py,sha256=JVkfMnRMiNtsZOqsXZYgGT6XhtXTti6qw7MINj3Rwmc,9065
+cool_seq_tool/mappers/__init__.py,sha256=5aE6IRTG8SwOofFR19QHmK-1n2PaKwEPzFGNE0_HS3s,261
+cool_seq_tool/mappers/alignment.py,sha256=htGb9rJab8dAKcMR62NF0uGc5l4KROrMcMAKfSQhva0,9620
+cool_seq_tool/mappers/exon_genomic_coords.py,sha256=BH3BIEUOrccjtqVxlkl-LQt5f8BXCvFmCJfVfb5qgYI,30863
+cool_seq_tool/mappers/mane_transcript.py,sha256=h7J4ip9HPhVvADqvWp5ZGT9257xymVkSJ3vj3YRzIws,49359
+cool_seq_tool/routers/__init__.py,sha256=x00Dq0LzqYoBPbipmyexLbAMUb7Udx8DozfwT-mJo1E,436
+cool_seq_tool/routers/default.py,sha256=F9NDKv7oiEz7Yk9BKAqhJxTBELpYLDhOqB8keRVtYkU,3937
+cool_seq_tool/routers/mane.py,sha256=CKXAwIQOyfEhEiRCVMqzDesbijkUIFnvxx8mKPyxDXk,3547
+cool_seq_tool/routers/mappings.py,sha256=I9hxriBlkv9vQp1l_17L-VxQSUJ9-IyLyqwXGue4axg,6091
+cool_seq_tool/sources/__init__.py,sha256=lERBM8cOqlJhYqz_DwOMV5FsWvMvQMbU1KQBxx_cz6M,303
+cool_seq_tool/sources/mane_transcript_mappings.py,sha256=Bah16WhfBk3Def3ehYvccR13lO90f8Bib8rj8zbszVs,3753
+cool_seq_tool/sources/transcript_mappings.py,sha256=Gz1PCf54RDApY5QfZqP8vm4iHCHLv-Ar4cy5Dj4cAe4,9797
+cool_seq_tool/sources/uta_database.py,sha256=DYAH0oxxURyRbeRLlD3AQOi4BiTIlZbzsI05Lt6x68Y,44007
+cool_seq_tool-0.4.0.dev1.dist-info/LICENSE,sha256=1jbnPcw_qmlDZyD_E_ebjWwjIvBgOD-1biodvBtSl1U,1072
+cool_seq_tool-0.4.0.dev1.dist-info/METADATA,sha256=8wTeGZAxB0D2bebhpIvdp05_ehWLEnV62po7ugBCJY0,5658
+cool_seq_tool-0.4.0.dev1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+cool_seq_tool-0.4.0.dev1.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.4.0.dev1.dist-info/RECORD,,

{cool_seq_tool-0.3.0.dev1.dist-info → cool_seq_tool-0.4.0.dev1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cool_seq_tool-0.3.0.dev1.dist-info/METADATA

@@ -1,187 +0,0 @@
-Metadata-Version: 2.1
-Name: cool-seq-tool
-Version: 0.3.0.dev1
-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.*
-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
-```

cool_seq_tool-0.3.0.dev1.dist-info/RECORD

@@ -1,29 +0,0 @@
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