Release History

Version Date Notes
v0.8.1 2021-04-09 Dropped species list embedded in intermediate TSV, assess needs DB now.
v0.8.0 2021-04-06 Revised genus/species columns in sample report. Added scripts/ folder.
v0.7.11 2021-03-30 assess now only at sample level. Abundance threshold in classify.
v0.7.10 2021-03-24 Pipeline includes fasta-nr command making non-redundant FASTA file.
v0.7.9 2021-03-15 Option to show unsequenced entries in summary sample report (-u).
v0.7.8 2021-03-11 Only import IUPAC DNA characters to DB. Fixed N. valdiviana in default DB.
v0.7.7 2021-02-24 Revised default ITS1 DB: NCBI Oomycetes, more curation & single isolates.
v0.7.6 2021-02-17 Replaced seq-import with curated-seq, used when building default DB.
v0.7.5 2021-02-16 Refined default DB by adjusting how genus-level NCBI import was trimmed.
v0.7.4 2021-02-15 Edit-graph genus-only labels. New 1s2g, 1s4g & 1s5g classifiers.
v0.7.3 2021-01-29 Updated NCBI import & taxonomy. New 1s3g classifier. Use cutadapt v3.0+.
v0.7.2 2020-10-06 Added ena-submit command for use with interactive ENA read submission.
v0.7.1 2020-09-29 Curated Phytophthora DB minor updates. Classifier output in edit-graph.
v0.7.0 2020-04-02 Read counts etc as a header in intermediate FASTA files; shown in reports.
v0.6.15 2020-03-12 Fix regression in read report column sorting.
v0.6.14 2020-03-12 Merge read-summary & sample-summary into new summary command.
v0.6.13 2020-03-09 New classifier method substr for testing with poorly trimmed DB content.
v0.6.12 2020-03-09 New advanced setting --merged-cache intended for multiple marker use.
v0.6.11 2020-03-02 Updated genus-level only NCBI import, restrict to those with 32bp leader.
v0.6.10 2020-02-24 Treat I (for inosine as in tRNA) in primers as N (IUPAC code for any base).
v0.6.9 2020-02-20 Allow pre-primer-trimmed FASTQ. Fixed row coloring when missing samples.
v0.6.8 2020-02-17 Metadata -x default now column 1. Fixed read report metadata captions.
v0.6.7 2020-02-13 Method in pipeline filenames; max sample abundance in read reports.
v0.6.6 2020-02-05 Coloring groups in sample-report. Can call assessment from pipeline.
v0.6.5 2020-01-27 Do --flip in prepare-reads using cutadapt v2.8 or later.
v0.6.4 2020-01-23 curated-import accepts primers. Reduced memory usage for onebp.
v0.6.3 2020-01-20 Treat NCBI taxonomy “includes” as synonyms, adds 396 new species aliases.
v0.6.2 2020-01-14 Memory optimisation to the default onebp classifier.
v0.6.1 2020-01-08 Requires at least Python 3.6 as now using f-strings (internal change only).
v0.6.0 2020-01-08 Stop discarding normally conserved 32bp start of Phytophthora ITS1 marker.
v0.5.8 2019-12-11 Correction to start of a P. parsiana curated sequence in our DB.
v0.5.7 2019-12-09 Replace min bit score with min percentage coverage in blast classifier.
v0.5.6 2019-12-04 Import species under “unclassified Phytophthora” as genus Phytophthora.
v0.5.5 2019-12-03 Updated NCBI taxonomy, adds Phytophthora caryae and P. pseudopolonica.
v0.5.4 2019-12-02 Only use HMM to detect synthetic read negative controls.
v0.5.3 2019-11-25 Replace HMM filter on importing to the database with length check only.
v0.5.2 2019-11-25 Removed redundant use of HMM filter in seq-import command.
v0.5.1 2019-11-22 Updated NCBI taxonomy, adds Phytophthora oreophila and P. cacuminis.
v0.5.0 2019-11-21 Only use HMM as a filter, not for trimming in DB import or classify steps.
v0.4.19 2019-11-19 Additional curated entries in default ITS1 database.
v0.4.18 2019-11-19 Reworked sample-summary table output, now samples vs species with Excel.
v0.4.17 2019-11-15 Control based minimum abundance threshold applied at folders level.
v0.4.16 2019-11-15 Bug fix in fasta-nr when using input records with descriptions.
v0.4.15 2019-11-04 Harmonised dump FASTA & curated-import with semi-colon separator.
v0.4.14 2019-10-23 Configurable FASTA entry separator for curated-import & ncbi-import.
v0.4.13 2019-10-22 Fix 5 cases missing A near end, ...CTGAAAACT to ...CTGAAAAACT.
v0.4.12 2019-10-22 Removed now unused legacy-import and database/legacy/ files.
v0.4.11 2019-10-21 Updated the curated DB entries, focused on truncated sequences.
v0.4.10 2019-10-21 New curated-import command, reworked handling of curated DB entries.
v0.4.9 2019-10-17 New sample-summary switch -q / --requiremeta. NetworkX v2.4 fix.
v0.4.8 2019-10-11 New fasta-nr command for use in alternatives to prepare-reads.
v0.4.7 2019-10-10 New --minlen & --maxlen args for prepare-reads and pipeline.
v0.4.6 2019-10-02 Forgot to include updated DB with the PyPI release.
v0.4.5 2019-10-02 Apply primer trimming to ncbi-import (crop if primers found).
v0.4.4 2019-10-02 New --hmm & --flip arguments for prepare-reads and pipeline.
v0.4.3 2019-09-26 New conflicts command reporting genus/species level conflicts in DB.
v0.4.2 2019-09-26 Drop clade from taxonomy table, require unique species entries.
v0.4.1 2019-09-16 Include NCBI strains/variants/etc and their synonyms as species synonyms.
v0.4.0 2019-09-12 NCBI taxonomy synonym support; taxonomy import defaults to all Oomycetes.
v0.3.12 2019-09-12 New thapbi_pict dump option -m / --minimal for DB comparison.
v0.3.11 2019-09-09 Updated default DB and tests to use September 2019 NCBI taxonomy.
v0.3.10 2019-09-05 Handle missing or empty input FASTQ files more gracefully.
v0.3.9 2019-08-14 Log BLAST bit score. Merge thapbi assess warnings, 3dp for ad-hoc loss.
v0.3.8 2019-08-09 The blast classifier now applies a minimum BLAST bit score of 100.
v0.3.7 2019-08-05 Added Python API to the main documentation.
v0.3.6 2019-07-19 Added Zenodo FASTQ link to worked example, now includes assess command.
v0.3.5 2019-07-12 Added missing T or CT to 11 of the legacy ITS1 sequences in the DB.
v0.3.4 2019-07-08 Worked example using woody hosts dataset from Riddell et al. (2019).
v0.3.3 2019-07-04 Fixed regression in group coloring for read-summary Excel output.
v0.3.2 2019-07-04 Read The Docs; use -i / --input consistently - no positional args.
v0.3.1 2019-06-27 Reformatted documentation to use reStructuredText rather than Markdown.
v0.3.0 2019-06-26 Include four gBlocks synthetic negative controls in DB and pipeline.
v0.2.6 2019-06-25 Phytophthora ITS1 HMM threshold now set within model file, not the code.
v0.2.5 2019-06-21 Include XGMML edit-graph (for Cytoscape use) in pipeline output.
v0.2.4 2019-06-21 Fixed 3 Hyaloperonospora also in Peronospora in default DB.
v0.2.3 2019-06-18 Sample count rather than total read abundance for node size in edit-graph.
v0.2.2 2019-06-12 New edit-graph command for use with Cytoscape etc, or PDF via GraphViz.
v0.2.1 2019-05-27 Cope better with multiple (short) ITS1 fragments during classification.
v0.2.0 2019-05-14 Limit ITS1 length, 100 to 250bp. Exclude uncultured NCBI entries from DB.
v0.1.12 2019-05-09 Sort read-summary output by species. Set coloring group at command line.
v0.1.11 2019-05-06 Excel output from read-summary with formatting applied.
v0.1.10 2019-05-03 Tweaking command line API, renamed plate-summary to read-summary.
v0.1.9 2019-05-02 Implemented pipeline subcommand (prepare reads, classify, and report).
v0.1.8 2019-05-01 Standard errors for missing external tools; versions logged in verbose mode.
v0.1.7 2019-05-01 Changed default classifier method from identity to more fuzzy onebp.
v0.1.6 2019-04-30 Include ready to use binary ITS1 database in source tar-ball & wheel files.
v0.1.5 2019-04-29 Reworked optional metadata integration and its display in summary reports.
v0.1.4 2019-04-25 Sort samples using the optional metadata fields requested in reports.
v0.1.3 2019-04-24 Can optionally display sample metadata from TSV file in summary reports.
v0.1.2 2019-04-17 Keep searching if onebp classifier perfect match is at genus-level only.
v0.1.1 2019-04-16 Expand default taxonomy and database from Peronosporaceae to Peronosporales.
v0.1.0 2019-04-04 Include a bundled ITS1 database.
v0.0.15 2019-04-03 Support for genus-level only entries in the database.
v0.0.14 2019-04-01 MD5 in dump output. Fixed importing sequences failing taxonomic validation.
v0.0.13 2019-03-22 Remove conserved 32bp when primer trim. Assess at sample level by default.
v0.0.12 2019-03-11 Fixed bug in swarmid classifier.
v0.0.11 2019-03-08 Speed up FASTQ preparation by using flash instead of pear v0.9.6.
v0.0.10 2019-03-06 Replace primer code allowing only 1bp differences with cutadapt.
v0.0.9 2019-03-05 Looks for expected primers, discards mismatches. Caches HMM files locally.
v0.0.8 2019-02-21 Fix multi-class TN under-counting. New loss metric, swarmid classifier.
v0.0.7 2019-02-12 Added plate-summary command, onebp classifier.
v0.0.6 2019-02-07 Misc. cleanup and import fixes.
v0.0.5 2019-02-06 Hamming Loss in assessment output.
v0.0.4 2019-01-24 Added seq-import command, blast classifier, multi-taxon predictions.
v0.0.3 2019-01-22 Simplified generated filenames.
v0.0.2 2019-01-21 Added assess command.
v0.0.1 2019-01-17 Initial framework with identity and swarm classifiers.