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.
3 maintainers
Release files for cool-seq-tool 0.17.0
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| cool_seq_tool-0.17.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 8.4 MB
Release files / cool_seq_tool-0.17.0.tar.gz
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