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Changelog

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

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

Version 1.5.2

Database

  • MASHix.py now has new filters to remove genes from plasmid database
  • Updated database with the latest ncbi refseq release (7/13/18, 5:27:00 AM)

New features

  • Now local installations of pATLAS can download data rather than making a request to patlas.site, which will fail.

Version 1.5.0

Database

  • Added new table to database in order to store temporary entries, containing results sent from POST requests that can be displayed using unique urls. This included:
    • Addition of front end capabilities to render results collected from the temporary database entries.
    • Addition of back end view that enables to handle the POST request and to make a GET from the pATLAS front end.

Requests

  • Now it is possible to make POST request to download metadata and sequences. Also, it is possible to make POST requests to view results from external tools.

Database naming refactor

  • Now database name should/can be provided to scripts that interact with psql database. E.g. of scripts that require this are: MASHix.py, db_create.py, run.py.

Bug fixes

  • fixed bug with assembly sample file import.
  • fixed bug when heatmap is called after filtering from a file, where the plasmid length data is missing for a plasmid from another file that is being compared with the current file in the heatmap.
  • fixed bug when unknown accessions are provided to the remove redundancy option.
  • fixed a bug when download button is triggered, centering again the graph.
  • fixed a bug on macOS and windows were window.open function added some type of "offset" to vivagraph canvas, removing window.open and adding a new way to download the sequences.

new features

  • added loader to slider buttons (buttons that allow to slide between files.
  • added check for popup blocking.
  • new function that allows to center on the node with more links
  • added new button to center on the node being displayed in the popup
  • added dynamic text to file inputs.

Version 1.4.1

Database update

  • Updated database to the plasmid NCBI refseq from 21/5/18.

    • updated vivagraph related json files to generate nodes and links.
    • updated json files to generate the dropdowns.
    • updated the psql database.
    • added new aro_index.csv to repo so that abricate2db.py can use it.

  • Blacklisted several oddities from the parser in taxa_fetch.py.

Bug fixes

backend

  • Several minor fixes to the MASHix.py script.
  • Patched the recursive function node_crawler in MASHix.py, allowing a higher number of recursive instances for this function.

frontend

  • Patched renderer after searching for a plasmid.

UX improvements

  • Improved readability of union and intersection legend, as well as, its modal.
  • Fixed popup_description

Version 1.4.0

New features

  • Adds redundancy removal option for mapping, mash screen and sequence imports.

  • Adds drag and drop of files to imports and projects menu.

  • Adds project export/import

  • Adds advanced filters

Documentation

  • Added docs for the new features.