Pathologic GenBank File Import Weirdness- Ptools v.23
These glitches concern ptools v 23.
I'm using Pathologic to convert GenBank .gbk files into PGDBs. I noticed a few problems detailed below.
1.In both desktop and web versions of ptools, the gene frames do not show the PGDB accessions, although the NCBI locus_tags are visible. That's a big problem for those of us using the PGDB accessions in downstream compute processes.
2.After running an initial Pathologic .gbk import (create overview checked at pathologic import step) followed by a save, the genome overview shows a bunch of black orfs, no color. Zooming in within the overview shows a white boxes, no color. The only way I could get the overview to look "normal" was to run hole filling. Rescoring pathways and /or Predict Transcription Units didn't correct the overview problem.
