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STANDARD OPERATING PROCEDURE: "Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Testing”
Citation:
Finnegan, C., D. Blatz, AND C. LaLone. STANDARD OPERATING PROCEDURE: "Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Testing”. U.S. Environmental Protection Agency, Washington, DC, 2021.
Impact/Purpose:
Standard Operating Procedure for testing every feature/function/dataset produced by SeqAPASS in a step by step manner.
Description:
The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) Standard Operating Procedure (SOP) has been developed to test all current functionality of SeqAPASS tool. It can be used at any time during development, however it is most critical when testing the code upon being dropped into the staging environment and the production environment. It is anticipated that as development of the SeqAPASS tool continues the SeqAPASS SOP will be updated to incorporate the most up to data features. Testing is divided into two components, first focusing on the Graphical User Interface (GUI; FrontEnd) and second the Data/Database (BackEnd). Depending on whether the SeqAPASS tool is moving toward a minor or major version release either one or both components of the tool may be tested. This testing SOP is organized by pages and features in the SeqAPASS tool as indicated by the header for each testing section. Testing of the SeqAPASS tool may begin at the beginning of the SOP and work through the complete SOP if the entire tool is moving into staging or production, or the testing may be conducted for select features that have been modified or changed during iterative development of the tool. Protein and taxonomy data from the National Center for Biotechnology Information (NCBI) databases are periodically retrieved and used to update the backend of SeqAPASS. R code has been developed to automate data comparisons between new and old data versions to check for anomalies. The source code that is used in R is provided at the end of the SOP. To run the R code, the tester must have R studio installed on their computer. Impact statement: Standard Operating Procedure for testing every feature/function/dataset produced by SeqAPASS in a step by step manner.