macarthur-lab/leiden_sc — pull request #2 by andrewhill157 (2014-03-19 16:32:17+00:00)
Title: Added module for remapping variants from HGVS to VCF format.

This code contains a new module macarthur_core/remapping. Genetic mutations are often listed in one of two formats, HGVS and VCF. HGVS is compact and has its own (relatively complex) syntax for describing mutations. However, for large scale analysis projects HGVS is extremely difficult to use effectively for a number of reasons. We want to convert data from the Leiden Open Variation Databases (the ones macarthur_core/lovd is designed to interact with) from one format to the other. This is a non-trivial conversion.

The class VariantRemapper macarthur_core/remapping/remapping.py basically wraps a third party module to make it easier to use within my project. The third party module documentation and description HGVS vs. VCF notation is described here: https://github.com/counsyl/hgvs

Unfortunately, this module depends on two relatively large files that I cannot easily host on github. These are normally housed in a folder called resources within the module. One is a human genome reference sequence (hg19.fa) and the other is a file containing definitions of transcript sequences that are needed to facilitate conversion between the HGVS and VCF (genes.refSeq). If you would like to actually run the code, then we will need get you these files some other way.