44. A laboratorian perspective on effective utility of Python programming for common bioinformatics laboratory tasks

Targeted computer programming is an effective laboratory skill that can be readily utilized by lab technologists to improve the efficiency and accuracy of laboratory tasks. Parsing, locating, and sorting files are everyday tasks which can be automated through targeted programming. Furthermore, commercially available software for specialized tasks, such as creating BED files for genomic analysis, can be limiting to specific lab objectives. To overcome these difficulties, lab technologists may need to learn programming skills in order to address individual lab needs without relying on IT personnel or bioinformaticians. Moreover, programming reduces human error, which may accumulate with manual procurement procedures. The Python computer language can be utilized to assist laboratory professionals and ease the burden of time-consuming tracking or repetitive tasks. It allows technologists to focus on the more pertinent task of analyzing patient data with consistency, efficiency and accuracy. Using our cytogenetics laboratory experience as an example, we will discuss the implementation of Python computer programming for our laboratory tasks. We will discuss (1) parsing information from several files to create a list of our patients that are on clinical trials which require special attention, (2) creating BED files combining Python programing with information on gene structure from UCSC Table Browser with disease specific gene lists, and (3) consolidating patient files based on disease type or other laboratory procedures. An overview of the basic structure of these Python programs used to accomplish these tasks and their effective implementation will be discussed. Lastly, we will present resources and concepts for practical application of computer programming in the laboratory setting.