THAPBI PICT v1.0.16

Released on PyPI 2024-09-09:

https://pypi.org/project/thapbi-pict/1.0.16/

Drops empty rows/columns (all zero read counts) in the reports when using --requiremeta or -q to hide samples without metadata.

This release also updates the default ITS1 database slightly, adopting the September 2024 NCBI taxonomy and adding a few more reference sequences affecting non-Phytophthora only.

THAPBI PICT v1.0.15

Released on PyPI 2024-09-05:

https://pypi.org/project/thapbi-pict/1.0.15/

Updated the default ITS1 database with additional curated entries, many from Jung et al. (2024), and the NCBI taxonomy as of August 2024. See:

Jung et al. (2024) Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity https://doi.org/10.3114/sim.2024.107.04

This included renaming our placeholder Phytophthora taxon ad7988a to Phytophthora sp. taxon castitis as per KC478759:

Bertier et al. (2013) The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops https://doi.org/10.3767%2F003158513X668554

THAPBI PICT v1.0.14

Released on PyPI 2024-08-26:

https://pypi.org/project/thapbi-pict/1.0.14/

Added a fifth synthetic control to the default DB, now used in the revised protocol at the Hutton Institute to construct mock-communities with magnitude steps in concentration, for use with the Illumina NextSeq and potentially higher read depth.

The pipeline and prepare-reads commands now support an optional -k or --markers argument to restrict the analysis to a subset of the markers defined in a multiple-marker database. An example use-case would be processing our historic MiSeq plates using ITS1 only when using a DB containing ITS1 and rps10 marker definitions. The default remains looking for all defined markers.

THAPBI PICT v1.0.13

Released on PyPI 2024-05-22:

https://pypi.org/project/thapbi-pict/1.0.13/

Updated the default Phytophthora focused ITS1 database with a more recent NCBI search, taxonomy, etc.

Stops using freeze-panes in Excel output which was no longer practical with small screens and/or lots of metadata.

THAPBI PICT v1.0.12

Released on PyPI on 2024-03-11:

https://pypi.org/project/thapbi-pict/1.0.12/

Fixes the inadvertent use of type-annotation syntax which had required Python 3.9 or later since THAPBI PICT v1.0.9. This release is tested on and requires at least Python 3.8.

Graceful edit-graph failure if missing graphviz fdp command line tool.

Heuristics for importing sequences in SINTAX style when missing genus in the species field.

Metadata argument -x now accepts multiple columns.

THAPBI PICT v1.0.11

Released on PyPI on 2024-03-05:

https://pypi.org/project/thapbi-pict/1.0.11/

Harmonised the ASV naming used in the optional FASTA and BIOM output files to match the main TSV and Excel usage. The sample-tally command and stage of the pipeline can now optionally output a BIOM file.

Importing the (pre-classifier) BIOM file and matching FASTA file of ASV sequences into Qiime2 has been tested.

THAPBI PICT v1.0.10

Released on PyPI on 2024-02-26:

https://pypi.org/project/thapbi-pict/1.0.10/

Changed sample report 'Unique' column to be the number of unique ASVs as per the expectation in the examples. Previously this showed the number of unique species or species complex classifications (a smaller number, although often close with good database coverage and a low diversity sample).

Adjusted the metadata counts in the read report to show 'Accepted' and 'Unique' in read report column headers, and replaced the old TOTAL row values (equal to the 'Accepted' values) with MAX values instead.

Use thousands separators in Excel for read counts etc. This should respect regional settings.

The import command now rejects species names with semi-colon in them, which would cause issues downstream as the semi-colon is used to separate multiple taxonomic matches.

Updated the gg_to_sintax.py helper script to accept FASTA and TSV input files from Qiime2 archives.

THAPBI PICT v1.0.9

Released on PyPI on 2024-02-12:

https://pypi.org/project/thapbi-pict/1.0.9/

Using Python type annotations (internal code change).

THAPBI PICT v1.0.8

Released on PyPI on 2024-02-06:

https://pypi.org/project/thapbi-pict/1.0.8/

Updated the default database with the February 2024 NCBI taxonomy (e.g. Phytophthora glovera is now P. gloveri).

Added several additional curated Phytophthora to the default ITS1 database, including 15 novel taxa which we have observed in multiple samples from the environment or tree nurseries, and KP691408.1 as Phytophthora taxon Catala2017sp4 from Català et al. (2017) https://doi.org/10.1111/ppa.12541

Corrected the year in the novel species entries like Phytophthora taxon Catala2015sp1 to match the citation Català et al. (2015) https://doi.org/10.1371/journal.pone.0119311

Also added a 1s6g classifier following the existing naming pattern.

THAPBI PICT v1.0.7

Released on PyPI on 2024-01-29:

https://pypi.org/project/thapbi-pict/1.0.7/

Updated the default database to treat Phytophthora cambivora as a synonym
of the more recent Phytophthora x cambivora description as a hybrid.

Also fixed the documentation builds on Read-The-Docs.