The following table lists a consise summary of the main changes in each release. Please see https://github.com/peterjc/thapbi-pict/releases for more detailed release notes.
| Version | Date | Notes |
|---|---|---|
| v1.0.17 | 2024-11-08 | Requires Python 3.10. Uses rich-argparse if installed for CLI colors. |
| v1.0.16 | 2024-09-09 | Hide any zero rows/cols in reports when using -q or --requiremeta. |
| v1.0.15 | 2024-09-05 | Additional curated entries in default DB, many from Jung et al. (2024). |
| v1.0.14 | 2024-08-26 | Added a fifth synthetic control to the default DB. |
| v1.0.13 | 2024-05-22 | Updated NCBI taxonomy and bulk genus-only entries in default DB. |
| v1.0.12 | 2024-03-11 | Restored Python 3.8 support. More robust import of SINTAX style FASTA files. |
| v1.0.11 | 2024-03-05 | Harmonize ASV naming in BIOM output, optional sample-tally BIOM output. |
| v1.0.10 | 2024-02-26 | Sample report 'Unique' column is now the unique ASV count. Misc updates. |
| v1.0.9 | 2024-02-12 | Using Python type annotations (internal code change). Python 3.9 onwards. |
| v1.0.8 | 2024-02-06 | Additional curated Phytophthora in default DB including 15 novel taxa. |
| v1.0.7 | 2024-01-29 | Treat Phytophthora cambivora as a synonym of Phytophthora x cambivora. |
| v1.0.6 | 2024-01-24 | Added some Peronosclerospora to curated DB. Updated NCBI import. |
| v1.0.5 | 2023-11-22 | Updated NCBI import, and scripted most of what was a semi-manual process. |
| v1.0.4 | 2023-11-20 | Dropped unused -m / --method argument to edit-graph command. |
| v1.0.3 | 2023-09-04 | Updated NCBI import and curated P. condilina entries in default DB. |
| v1.0.2 | 2023-08-18 | Use sum of cutadapt and singleton values etc for pooled marker reports. |
| v1.0.1 | 2023-07-26 | Fixed some rare corner-case read-corrections in unoise-l mode. |
| v1.0.0 | 2023-05-19 | Minor documentation changes, linked to Cock et al. (2023) preprint. |
| v0.14.1 | 2023-03-13 | Optional BIOM output using the biom-format Python library. |
| v0.14.0 | 2023-03-02 | Offers UNOISE read-correction, built-in or invoking USEARCH or VSEARCH. |
| v0.13.6 | 2022-12-28 | Factional abundance threshold in sample-tally was not strict enough. |
| v0.13.5 | 2022-12-21 | Misc small fixes and documentation updates. |
| v0.13.4 | 2022-12-07 | Support abundance thresholding in the sample-tally step. Log controls. |
| v0.13.3 | 2022-11-25 | Using new sample-tally command in pipeline, not fasta-nr. |
| v0.13.2 | 2022-11-11 | Sped up substr classifier, especially with larger databases. |
| v0.13.1 | 2022-09-21 | Minor default DB update. Cap --cpu by available CPUs. Faster DB import. |
| v0.13.0 | 2022-09-14 | Sped up distance based classifiers by better use of RapidFuzz library. |
| v0.12.9 | 2022-08-19 | Updates default DB with new curated species and improved left trimming. |
| v0.12.8 | 2022-08-08 | Treat NCBI taxonomy 'equivalent name' as a synonym. Minor DB update. |
| v0.12.7 | 2022-07-26 | NCBI taxid in genus-only fallback classifier output. Minor DB update. |
| v0.12.6 | 2022-07-25 | Changes to how NCBI sequences are trimmed for use in the default DB. |
| v0.12.5 | 2022-07-08 | Merged/child NCBI taxid entries as synonyms. Import FASTA with taxid. |
| v0.12.4 | 2022-07-07 | Updated edit-graph code to work with RapidFuzz v2.0.0 or later. |
| v0.12.3 | 2022-07-06 | Updated NCBI taxonomy and bulk genus-only entries in default DB. |
| v0.12.2 | 2022-06-15 | Updates to the curated entries in the default Phytophthora ITS1 DB. |
| v0.12.1 | 2022-05-18 | Fix missing field regression on reports including unsequenced samples. |
| v0.12.0 | 2022-04-19 | Set fractional abundance threshold via synthetic spike-ins. Cutadapt v4.0+. |
| v0.11.6 | 2022-03-09 | Fix regression on reports including unsequenced samples. |
| v0.11.5 | 2022-02-18 | Reporting enhancements when using spike-in (synthetic) controls. |
| v0.11.4 | 2022-02-08 | Updates to default curated DB, adding several more Phytophthora species. |
| v0.11.3 | 2022-02-01 | Fix dynamic k-mer threshold for synthetic spike-in control sequences. |
| v0.11.2 | 2022-01-20 | Windows testing on AppVeyor, with minor Windows specific fixes. |
| v0.11.1 | 2022-01-18 | Using rapidfuzz rather than python-Levenshtein. |
| v0.11.0 | 2022-01-13 | Multi-marker reports, pooling predictions from each marker. |
| v0.10.6 | 2022-01-12 | Fixed slow-down in v0.10.0 on large datasets with small DB. |
| v0.10.5 | 2021-12-23 | Default for -f / --abundance-fraction is now 0.001, meaning 0.1%. |
| v0.10.4 | 2021-11-24 | Updates to default curated DB, including newer NCBI taxonomy. |
| v0.10.3 | 2021-11-19 | New -f / --abundance-fraction setting, off by default. |
| v0.10.2 | 2021-11-05 | Updates to default curated DB. Small changes to NCBI taxonomy loading. |
| v0.10.1 | 2021-07-28 | Fix for using SQLAlchemy v1.3 (previous release needed v1.4). |
| v0.10.0 | 2021-07-28 | Rework to handle larger DB and multiple markers. Modifies DB schema. |
| v0.9.9 | 2021-07-08 | Drop SWARM based classifiers. Single intermediate TSV file in pipeline. |
| v0.9.8 | 2021-06-17 | Drop edit-graph in pipeline. Require full length primers in merged reads. |
| v0.9.7 | 2021-06-04 | USEARCH SINTAX & OBITools FASTA conventions in import command. |
| v0.9.6 | 2021-05-21 | Update default DB taxonomy, Peronosporales & Pythiales max 450bp. |
| v0.9.5 | 2021-05-10 | Simplify to just one import command for pre-trimmed FASTA input. |
| v0.9.4 | 2021-05-05 | Drop unused metadata fields in DB schema. Fix GML format edit graphs. |
| v0.9.3 | 2021-05-04 | Drop HMM for spike-in control detection, now via DB & k-mer counting. |
| v0.9.2 | 2021-04-28 | Fix obscure problem using relative versions of absolute paths. |
| v0.9.1 | 2021-04-20 | Set metadata encoding. Spike-in HMM default now off. |
| v0.9.0 | 2021-04-19 | Drop use of Trimmomatic, faster and slightly higher read counts. |
| v0.8.4 | 2021-04-13 | Sped up re-running by delaying method setup until and if required. |
| v0.8.3 | 2021-04-13 | Include abundance threshold in summary reports (if varied by sample). |
| v0.8.2 | 2021-04-13 | Sample report pooling script. Fix -p in prepare-reads. |
| v0.8.1 | 2021-04-09 | Drop species list embedded in intermediate TSV, assess needs DB now. |
| v0.8.0 | 2021-04-06 | Revise genus/species columns in sample report. Add 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. Fix N. valdiviana in default DB. |
| v0.7.7 | 2021-02-24 | Revise default ITS1 DB: NCBI Oomycetes, more curation & single isolates. |
| v0.7.6 | 2021-02-17 | curated-seq replaces seq-import, used when building default DB. |
| v0.7.5 | 2021-02-16 | Refine default DB by adjusting how genus-level NCBI import trimmed. |
| v0.7.4 | 2021-02-15 | Edit-graph genus-only labels. New 1s2g, 1s4g & 1s5g classifiers. |
| v0.7.3 | 2021-01-29 | Update NCBI import, taxonomy. New 1s3g classifier. Use cutadapt v3.0+. |
| v0.7.2 | 2020-10-06 | New 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 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 | Update 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. Fix row coloring when missing samples. |
| v0.6.8 | 2020-02-17 | Metadata -x default now column 1. Fix 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. Reduce memory usage for onebp. |
| v0.6.3 | 2020-01-20 | Treat NCBI taxonomy "includes" as synonyms, 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 Phytophthora ITS1 marker 32bp start. |
| 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 | Update 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 | Remove redundant use of HMM filter in seq-import command. |
| v0.5.1 | 2019-11-22 | Update 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 | Rework 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 | Harmonise 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 | Remove now unused legacy-import and database/legacy/ files. |
| v0.4.11 | 2019-10-21 | Update curated DB entries, focused on truncated sequences. |
| v0.4.10 | 2019-10-21 | New curated-import command, rework 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 reports 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 & their synonyms as species synonyms. |
| v0.4.0 | 2019-09-12 | NCBI taxonomy synonym support; Oomycetes default taxonomy import. |
| v0.3.12 | 2019-09-12 | New dump option -m / --minimal for DB comparison. |
| v0.3.11 | 2019-09-09 | Update 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 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 | Add Python API to the main documentation. |
| v0.3.6 | 2019-07-19 | Add Zenodo FASTQ link to worked example and use assess command. |
| v0.3.5 | 2019-07-12 | Add 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 | Fix 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 | Reformat 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 set within model file, not in code. |
| v0.2.5 | 2019-06-21 | Include XGMML edit-graph (for Cytoscape use) in pipeline output. |
| v0.2.4 | 2019-06-21 | Fix 3 Hyaloperonospora also in Peronospora in default DB. |
| v0.2.3 | 2019-06-18 | Sample count rather than total read abundance for edit-graph node size. |
| v0.2.2 | 2019-06-12 | New edit-graph command. Use 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, 100-250bp. Exclude uncultured NCBI entries from DB. |
| v0.1.12 | 2019-05-09 | Sort read-summary 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 | Tweak command line API, renamed plate-summary to read-summary. |
| v0.1.9 | 2019-05-02 | New pipeline subcommand (prepare reads, classify, and report). |
| v0.1.8 | 2019-05-01 | Standard errors for missing external tools. Log versions in verbose mode. |
| v0.1.7 | 2019-05-01 | Chang default classifier method from identity to more fuzzy onebp. |
| v0.1.6 | 2019-04-30 | Include ready to use binary ITS1 DB in source tar-ball & wheel files. |
| v0.1.5 | 2019-04-29 | Rework 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 & DB from Peronosporaceae to Peronosporales. |
| v0.1.0 | 2019-04-04 | Include a bundled ITS1 DB. |
| v0.0.15 | 2019-04-03 | Support for genus-level only entries in the DB. |
| v0.0.14 | 2019-04-01 | MD5 in dump output. Fix importing sequences failing taxonomic validation. |
| v0.0.13 | 2019-03-22 | Drop conserved 32bp when primer trim. Assess at sample level by default. |
| v0.0.12 | 2019-03-11 | Fix bug in swarmid classifier. |
| v0.0.11 | 2019-03-08 | Sped 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 | Look for expected primers, discards mismatches. Cache 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 | New 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 | New seq-import command, blast classifier, multi-taxon predictions. |
| v0.0.3 | 2019-01-22 | Simplify generated filenames. |
| v0.0.2 | 2019-01-21 | New assess command. |
| v0.0.1 | 2019-01-17 | Initial framework with identity and swarm classifiers. |