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
>>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
>>> 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.
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