Added ability to set the geneID and refSeqID parameters by passing at command line. Now additionally writes out only the protein change column to a separate file, which can be passed as is to mutalyzer for remapping. Minor changes to file name construction method.
Fixed indenting.
New script to combine and process raw Leiden data and Mutalyzer output. Replaces OpenRefine recipe and makes process much more automated.
Bug fix: only second digit of two digit chromosome numbers was being extracted. Now uses regex which is more robust.
Minor bug fix, lines in file were being written multiple times. May have caused errors, but may have just degraded performance.
Corrected indent.
_MAPPED now appears at end of results file name, rather than at the beginning.
Updated documentation (in progress)
Corrected bugs in chromosome number and coordinate extraction from HVGS notation. Previously, not all digits were always being captured.
Added error handling to allow batches to process even if one file has an error (errors are reported). Command line interface now allows either specifying files or operation on all files in directory.
Added ability to automatically determine transcriptRefSeqID from gene ID (no longer have to pass to constructor). Also added ability to extract all genes in DB (no arguments) or pass geneIDs as command line arguments in __init__.py
Added documentation. Not yet complete.
Moved files to different directory. Bug fix: corrected bug where DNA change column was not being correctly outputted to MutalizerInput file. This was a result of inconsistent column order between databases. Column headers are now used to determine the correct column.
Big fix: command line interface not working for specifying multiple geneIDs. Can now pass a list of genesIDs to extract data for.
Added improved command line interface to allow processing of all files in the directory or a list of specified files.
Stopped tracking files.