TODO: Upload.

Add "Was not best match" to unmapped reasons.
Sort unmapped reasons.

TODO:

  1. Pick only the best Xrefs of those that pass the thresholds.
  2. Store new analysis (if needed).
  3. Do the upload of the tables.

Slight formatting.

Still to do:

  1. Write 'unmapped_reason'.
  2. Write 'unmapped_object'.
  3. Upload.

All output to screen for now.

Only contains stubs at the moment.

Add hooks into coordinate mapping code.

standard option names added

Comment changes.

UCSC.

the add_xref() method for coordinate-based Xrefs.

Based on the knownGenes table from UCSC.

added get_all_Genes_by_source and made get_all_Genes_by type select at teh sql level rather than later on using grep