Common Operation on Lots of Sequences Tool

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  • License: MIT License (MIT License)
  • Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
  • Requires: Python >=3.10
  • Provides-Extra: dev, tests, docs
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Project description

Cool-Seq-Tool

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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.

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