README.md

CoolSeqTool

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Documentation · Installation · Usage · API reference

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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

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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.

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Usage

All CoolSeqTool 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'>)

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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.