pycircdb：面向计算工作流的整合型 circRNA 数据库注释工具
pycircdb: integrated circRNA database annotation for computational workflows
pycircdb 是一个 Python 命令行工具，可输入人类 circRNA 基因组坐标，快速查询多个经整理的 circRNA 数据库并输出可复现注释。各数据库已统一为 0-based 表示并在 hg19 与 hg38 组装间交叉映射，兼容 0-based 和 1-based 坐标输入，采用容错匹配策略。
来源：Bioinformatics Advances · doi.org
Motivation
Currently, multiple databases exist for the annotation of circular RNAs, providing descriptions of their genomic features, FASTA sequences, predicted microRNA targets and RNA-binding protein interactions. Despite the availability of these resources, annotation remains cumbersome. Conflicting identifiers and genomic coordinates for circular RNAs across databases pose a challenge to reproducibility for users. Furthermore, current databases primarily provide access via web-based graphical user interfaces, bulk downloads and limited programmatic access, rendering their use in computational workflows challenging.
Results
We present pycircdb, a Python command-line interface tool that accepts genomic coordinates of human circular RNAs as input, facilitating rapid queries of multiple curated circRNA databases for reproducible annotation. Each pycircdb database has been normalised to a common 0-based representation and cross-mapped between the hg19 and hg38 assemblies, accepting as input circular RNA coordinates from 0-based and 1-based sources using a tolerant matching strategy. pycircdb utilises Apache Hamilton in conjunction with Parquet files, providing a modular, parallelised workflow with minimal disk space requirements.
Availability
pycircdb is available for download via PyPI https://pypi.org/project/pycircdb under the GPL-3.0 license with source code and documentation available at https://github.com/BarryDigby/pycircdb and https://pycircdb.readthedocs.io/en/latest, respectively.