Pynoma, PyABraOM and BIOVARS: Towards genetic variant data acquisition and integration
MotivationAdvances in genomic sequencing of human populations have generated a large amount of genomics data deposited in multiple sources. Programmatic batch searches executed at once are of great scientific interest to ease genomic investigations by retrieving and integrating this massive and decentralized data with little manual intervention. ResultsPynoma and PyABraOM APIs were developed to offer multiple queries in gnomAD and ABraOM databases, respectively. A centralized search in these databases with data integration is offered by a third API, BIOVARS, which combines the resulting information with statistical and graphical visualizations. The implemented features are demonstrated in a case study using ACE2, ADAM17 and TMPRSS2 genes, which presents a generalizable workflow that shows how our APIs facilitate the access and integration of valuable biological data. AvailabilityAll the APIs are written in Python 3. Graphical visualizations for the retrieved data are provided by using the R language version 4.1. The source codes are publicly available and hosted on GitHub (github.com/bioinfo-hcpa). Contactumatte@hcpa.edu.br Supplementary informationSupplementary data is available at github@nbioinfo-hcpa.