Common Operation on Lots of Sequences Tool
Verified details
These details have been verified by PyPIProject links
GitHub Statistics
Maintainers
Project description
Cool-Seq-Tool
Documentation · Installation · Usage · API reference
Overview
The Common Operations On Lots-Of Sequences Tool, Cool-Seq-Tool, 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 transcript alignment data from the Universal Transcript Archive
- Augmented access to the SeqRepo database, including multiple additional methods and tools
- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined here, that combine the above to support translation between references sequences, annotation layers, and transcripts
Install
Cool-Seq-Tool 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 Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
>>> from cool_seq_tool import CoolSeqTool
>>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
>>> cst = CoolSeqTool()
>>> result = await cst.mane_transcript.get_mane_transcript(
... "NP_004324.2",
... 599,
... AnnotationLayer.PROTEIN,
... coordinate_type=CoordinateType.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.
Project details
Verified details
These details have been verified by PyPIProject links
GitHub Statistics
Maintainers
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
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file cool_seq_tool-0.15.3.tar.gz.
File metadata
- Download URL: cool_seq_tool-0.15.3.tar.gz
- Upload date:
- Size: 4.4 MB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
74bb10e4db9c77f5fa1e3e44c346bdd4971a46dc84666ede21eaf85115a082db
|
|
| MD5 |
a20b3940c420c6efdcef18979dbd4965
|
|
| BLAKE2b-256 |
8ff3cc0c0241e9df001e71ae5622a5a1d0b22ac0fb8d1f7a43832d7136a5a610
|
Provenance
The following attestation bundles were made for cool_seq_tool-0.15.3.tar.gz:
Publisher:
release.yml on GenomicMedLab/cool-seq-tool
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cool_seq_tool-0.15.3.tar.gz -
Subject digest:
74bb10e4db9c77f5fa1e3e44c346bdd4971a46dc84666ede21eaf85115a082db - Sigstore transparency entry: 846502715
- Sigstore integration time:
-
Permalink:
GenomicMedLab/cool-seq-tool@7e3a95dec6840569aa81e22b13126514988f42e8 -
Branch / Tag:
refs/tags/0.15.3 - Owner: https://github.com/GenomicMedLab
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
release.yml@7e3a95dec6840569aa81e22b13126514988f42e8 -
Trigger Event:
release
-
Statement type:
File details
Details for the file cool_seq_tool-0.15.3-py3-none-any.whl.
File metadata
- Download URL: cool_seq_tool-0.15.3-py3-none-any.whl
- Upload date:
- Size: 4.0 MB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
9c7ffe854674b53cc1c392f7bda49553d3a979b30e60bf7cfceba3cdafebd317
|
|
| MD5 |
f23b5569b5b829c2d9246f039cd3f507
|
|
| BLAKE2b-256 |
d1d29e4df596a2586bed4d912e50c25ee5c1e2fb2d70e079962451319ef169cb
|
Provenance
The following attestation bundles were made for cool_seq_tool-0.15.3-py3-none-any.whl:
Publisher:
release.yml on GenomicMedLab/cool-seq-tool
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
cool_seq_tool-0.15.3-py3-none-any.whl -
Subject digest:
9c7ffe854674b53cc1c392f7bda49553d3a979b30e60bf7cfceba3cdafebd317 - Sigstore transparency entry: 846502796
- Sigstore integration time:
-
Permalink:
GenomicMedLab/cool-seq-tool@7e3a95dec6840569aa81e22b13126514988f42e8 -
Branch / Tag:
refs/tags/0.15.3 - Owner: https://github.com/GenomicMedLab
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
release.yml@7e3a95dec6840569aa81e22b13126514988f42e8 -
Trigger Event:
release
-
Statement type:
