Charizard

Version 1.6.1

Back end

• Added bacmet implementation for the backend (resources, views and models)
• Added a new script called diamond2db.py which enables to send bacmet results to the database table.

Front end

• Added implementation of bacmet for the statistics, browsing, tables and popups

Charmelleon

Version 1.6.0

Back end

• Added code that allows to save a list of all the accession numbers to a file,
  so that future changes to the database can be easily documented.
• Added black list for accession numbers that are reported to be misplaced as
  plasmids in refseq database.
• Update database to NCBI refseq 091418.
• Added first implementation to parse result from plasmidfinder new database.

Front end

Database queries

• Search for accession numbers now accept accession without version
  (e.g NC_011413).

Import results

• Import from file and requests now have an option to submit and filter
  directly.
• Import from file now has option that allows the user to select the sample to
  display.

Performance

• Performance of the page was significantly improved with the fix of issue #57.
• Welcome modal was temporarily hidden.
• Refactored defaultZooming function, now showing only the final zoom.

Other changes

• Added default behavior for close buttons in modals for imports.
• Added small information messages to loading.
• Shift key drag selections now accept multiple selected areas and drag of
  multiple nodes.
• Improved modals text and several formatting options were changed throughout
  modals.
• Implemented highlight and filter for all node selections (taxa, resistances,
  plasmid families, virulence and combined selections).
• Added faq on how to report sequences that aren't plasmids.
• Removed histogram from length plot.
• Added new button that allow users to more easily report a sequence, by using
  github api for pre-filled issues.

Bug fixes

• Fixed minor issues after filtering datasets for link selections and for shift
  selections.
• Fixed bug with when file is imported preventing selections of taxa,
  resistance, plasmidfinder, virulence and so on.
• Fixed parsing of resistance genes that contained ' in their gene names

---

This release also adds a file with all the entries that were removed from NCBI RefSeq database for the pATLAS database (by the curation methods used) - available in removed_entries_stats.txt.

Charmander

This is the first official release of pATLAS featuring an up to date database and lots of goodies to explore this database. Enjoy browsing plasmids with pATLAS!

This release also includes the sql file that can be user to generate the database locally or to migrate between machines.