13th IHWS Shared Resources Joint
Alex K. Lancaster, Mark P. Nelson, Richard M. Single, Diogo Meyer, Glenys J. Thomson · 2004
The PyPop (Python for Population Genetics) analysis package is a suite of population genetic analyses and forms the base of the biostatistics core. It is in an object-oriented framework implemented in the programming language Python. The object-oriented approach allows us to implement individual analysis modules which can be inserted or removed without affecting other modules. Python is a flexible scripting language which allows rapid prototyping of code and has powerful features for interfacing with other languages, such as C (in which we have already implemented many routines and which is particularly suited to computationally intensive tasks). The output of the analyses are stored in the XML format (XML is the eXtensible Markup Language devised by the World Wide Web Consortium, and is a platform-independent, vendor-neutral, non-proprietary, open standard for storing data (2). These output files can then be transformed using standard tools into many other data formats suitable for machine input (such as PHYLIP (6) or input for spreadsheet programs such as Excel or statistical packages, such as R (8)), plain text, or HTML for ‘‘human-readable’’ format. Storing the output in XML allows the final viewable output format to be redesigned at will, without requiring the (often timeconsuming) re-running of the analyses themselves. Data from the anthropology, transplantation, disease and cytokine components have been analyzed using PyPop.