Changed process_annotated_mutations.py to write out tab delimited files with errors. Made utilities module with functions rather than inner class. Moved write_output_file to utilities.
Removed certain functions that were not particularly useful, such as getting trivial INFO column tags. Added functionality to display chromosome, ref, alt, and link to UCSC view of coordinate for discordant mutations.
Added working remapping using offline code from counsyl. Required resources are located in /lovd/remapping/resources. Includes genome reference FASTA and refseq list.
Modified scripts to use new remapping functionality from Counsyl. Ported to python 2.7 compatible code to enable use of required tools.
Added function to remap from VCF to HGVS.
General code cleanup and minor refactoring - particularly of VCF file text generation.
Updated script to use modified remapping libraries. Also added two command line parameters so that you can specify what the column labels for the hgvs notation and protein change columns are. This allows it to be applied to any tab-delimited file containing this information. May want to specify flags on command line for these rather than purely using the order.
Bug fix where modified VCF file generation messed up the header line formatting (added many additional tab characters). General code cleanup and some added documentation.
Fixed bug in file writing function where unicode strings were not properly decoded before writing out. This is unique to python 2 and was not an issue due to all unicode policy in python 3 (handles this decoding automatically). Other minor cleanup and documentation updates.
Updated refseq definitions to provide more reference transcripts. Added additional scripts to convert downloads from UCSC to usable formats and merge new and old definitions if updates needed in the future.
Updated command line interfaces to be more robust and include additional options. General code cleanup and documentation.
Minor refactoring, updated documentation, and reorganization of files within core module. Added function to read table data from files.
Added libraries to handle annotation of files and lsf commands on specifically on the braod cluster.
Modified file writng and reading functions to be more robust to large files (csv module is no longer used)
Moved modules around to make more sense as core library structure. Modified imports as needed.
Added new function to produce a VCF file from file with HGVS notation variants.
Separated HGVS and 26K annotation with VCF tools into two separate functions.
Restored resource files for remapping. Were accidentally deleted when creating separate set of core libraries.
Ignored hg19 reference files, as they are too large to put in version control.