| 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. |