Common Operation on Lots of Sequences Tool
Project description
CoolSeqTool
Documentation · Installation · Usage · API reference
Overview
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 descriptions, and the Universal Transcript Archive
- Augmented access to the 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
Install
CoolSeqTool is available on PyPI
python3 -m pip install cool-seq-tool
See the installation instructions 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:
>>> 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 contains guidance for submitting feedback and contributing new code.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file cool_seq_tool-0.4.0.dev1.tar.gz.
File metadata
- Download URL: cool_seq_tool-0.4.0.dev1.tar.gz
- Upload date:
- Size: 4.0 MB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/4.0.2 CPython/3.11.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 2f6ce9783829d2e057d5da772963816cae513958c0901120856dc2182293c6eb |
|
| MD5 | 2abda3b6bae961400514871f27549844 |
|
| BLAKE2b-256 | f9dfcbf08c89ed7edc071b8bb655cbe3086001b4e107334e9b1a2ad8bb1f4abc |
File details
Details for the file cool_seq_tool-0.4.0.dev1-py3-none-any.whl.
File metadata
- Download URL: cool_seq_tool-0.4.0.dev1-py3-none-any.whl
- Upload date:
- Size: 4.0 MB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/4.0.2 CPython/3.11.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 5b79eb7dcaa58f747c56c91746d707da1c7ef8d23c11a43c0a71cb97ba426da0 |
|
| MD5 | 2849609076634a22c7e0c4c03013a21c |
|
| BLAKE2b-256 | 888aca03b2963a6281cb162d65ad38d58b41024825cc103916aac6c9a0b517cd |
