Large-scale ID panel from de la Puente, Phillips, et al 2020 paper #49
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This update changes the "lab designator" from PP (Puente/Phillips) to USC (Universidade de Santiago de Compostela) for the marker collection most recently added to MicroHapDB in #49.
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This update brings in 118 additional marker definitions published recently by de la Puente, Phillips, and colleagues in FSI: Genetics. The marker definitions are provided in Supplementary File S1 of the paper. I used pdfminer to extract the text from this file, and then wrote
text2table.pyto organize the data into a tabular format with one row per marker. Finally,Snakefiledefines a brief Snakemake workflow for using rsIDs to grab the GRCh38 coordinates of each marker and compiling the marker definitions into the format required by MicroHapDB.NOTE: Four rsIDs needed manual attention during pre-processing.
This update also drops pytest as an install dependency. Closes #41.
A special thanks to Chris Phillips for responding to queries about this work!