peterjc/thapbi-pict issues and pull requests

#545 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#544 - Use 'unoise-l' to be explict about Levenshtein distance UNOISE

Pull Request - State: closed - Opened by peterjc over 1 year ago

#543 - Wrap vsearch and usearch for UNOISE read-correction

Pull Request - State: closed - Opened by peterjc over 1 year ago - 2 comments

#542 - Finish UNOISE distance-based greedy clustering (DGC)

Pull Request - State: closed - Opened by peterjc over 1 year ago

#541 - Add UNOISE alpha and gamma to command line

Pull Request - State: closed - Opened by peterjc over 1 year ago - 3 comments

#540 - Assess soil nematodes

Pull Request - State: closed - Opened by peterjc over 1 year ago

#539 - Discussion for soil_nematodes example

Issue - State: closed - Opened by peterjc over 1 year ago - 2 comments

#538 - UNOISE within sample-tally step

Pull Request - State: closed - Opened by peterjc over 1 year ago - 6 comments

#537 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#536 - Ignore controls not part of the input argument

Pull Request - State: closed - Opened by peterjc almost 2 years ago - 1 comment

#535 - Only apply abundance threshold in sample-tally

Pull Request - State: closed - Opened by peterjc almost 2 years ago - 2 comments

#534 - Record which samples are controls

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#533 - Apply min_abundance in parse_sample_tsv

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#532 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#531 - Record control status in sample-tally outputs

Issue - State: closed - Opened by peterjc almost 2 years ago
Labels: enhancement

#530 - Apply minimum total abundance in sample-tally

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#529 - Use sample-tally TSV in place of FASTA inputs to edit-graph

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#528 - Use samples-tally TSV in the assess command

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#527 - Abundance thresholding in sample-tally

Pull Request - State: closed - Opened by peterjc almost 2 years ago - 1 comment

#526 - Use 'python -m build' to make tar-ball and wheel

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#525 - Update to Oct 2022 NCBI taxonomy; no DB changes

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#524 - Supplement <stem>.all_reads.fasta with <stem>.tally.tsv

Pull Request - State: closed - Opened by peterjc almost 2 years ago - 1 comment

#523 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#522 - Refactor to centralise writing classifier output

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#521 - Always replace classifier output

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#520 - BIOM table export

Issue - State: closed - Opened by peterjc almost 2 years ago - 4 comments
Labels: enhancement

#519 - assess command slow with large DB

Issue - State: open - Opened by peterjc almost 2 years ago
Labels: enhancement

#518 - Update to Oct 2022 NCBI taxonomy; no DB changes

Pull Request - State: closed - Opened by peterjc almost 2 years ago

#517 - Segmentation fault from rapidfuzz-2.11.0

Issue - State: closed - Opened by peterjc almost 2 years ago - 2 comments

#516 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 2 comments

#515 - Pest insects worked example, Batovska et al. (2021)

Pull Request - State: closed - Opened by peterjc about 2 years ago - 6 comments

#514 - How to handle species without a genus?

Issue - State: open - Opened by peterjc about 2 years ago - 2 comments
Labels: enhancement

#513 - Speedup substr classifier

Pull Request - State: closed - Opened by peterjc about 2 years ago - 1 comment

#512 - Use more bulk DB importing

Pull Request - State: closed - Opened by peterjc about 2 years ago - 3 comments

#511 - Update to NCBI results from 2022-09-16

Pull Request - State: closed - Opened by peterjc about 2 years ago

#510 - Cap tools by available CPUs

Pull Request - State: closed - Opened by peterjc about 2 years ago

#509 - Accept .fq or .fq.gz in addition to .fastq(.gz)

Pull Request - State: closed - Opened by peterjc about 2 years ago

#508 - Bulk import with SQLalchemy

Pull Request - State: closed - Opened by peterjc about 2 years ago - 3 comments

#507 - DB import scales poorly with large datasets

Issue - State: closed - Opened by peterjc about 2 years ago - 6 comments
Labels: enhancement

#506 - Use single RapidFuzz cdist call instead of variant clouds

Pull Request - State: closed - Opened by peterjc about 2 years ago - 4 comments

#505 - Use RapidFuzz cdist instead of Levenshtein distance in inner loop

Pull Request - State: closed - Opened by peterjc about 2 years ago - 1 comment

#504 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago - 2 comments

#503 - Clarify incremental updates to Oomycota_ITS1_obs.fasta

Issue - State: closed - Opened by peterjc about 2 years ago - 1 comment

#502 - Add new curated Phytophthora entries from Jung et al 2022

Pull Request - State: closed - Opened by peterjc about 2 years ago - 1 comment

#501 - Update NCBI search as of 2022-08-17

Pull Request - State: closed - Opened by peterjc about 2 years ago

#500 - Add new curated Phytophthora entries from Jung et al 2022

Issue - State: closed - Opened by peterjc about 2 years ago - 2 comments

#499 - Insert missing T or TT from start of NCBI seqs; stricter 32bp check

Pull Request - State: closed - Opened by peterjc about 2 years ago - 1 comment

#498 - Require 31bp overlap with 32bp leader

Pull Request - State: closed - Opened by peterjc about 2 years ago - 1 comment

#497 - Improving left trimming in yyyy-mm-dd_ITS1_Oomycota_w32.fasta

Issue - State: closed - Opened by peterjc about 2 years ago - 5 comments

#496 - [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#495 - Drop Pythium from NCBI uncurated import?

Pull Request - State: closed - Opened by peterjc about 2 years ago - 3 comments

#494 - Treat NCBI taxonomy "equivalent name" as a synonym

Pull Request - State: closed - Opened by peterjc about 2 years ago

#493 - Should treat "equivalent name" as a synonym

Issue - State: closed - Opened by peterjc about 2 years ago - 1 comment
Labels: bug

#492 - Drop length restrictions for importing observed NCBI sequences

Pull Request - State: closed - Opened by peterjc about 2 years ago

#491 - Reduce minimum length for observed DB entries

Issue - State: closed - Opened by peterjc about 2 years ago - 2 comments

#490 - Fix side effects of ad-hoc removal of problematic accessions

Pull Request - State: closed - Opened by peterjc about 2 years ago

#489 - Ad hoc removal of accessions side effects

Issue - State: closed - Opened by peterjc about 2 years ago
Labels: bug

#488 - Lookup taxid for genus fallback in 1sXg classifiers

Pull Request - State: closed - Opened by peterjc about 2 years ago

#487 - Missing taxid for genus only fallback in 1s3g etc

Issue - State: closed - Opened by peterjc about 2 years ago
Labels: bug

#486 - Export taxid in FASTA DB dump; track this not SQL

Pull Request - State: closed - Opened by peterjc about 2 years ago - 1 comment

#485 - Strict right primer trimming on NCBI imports for default DB

Pull Request - State: closed - Opened by peterjc about 2 years ago - 3 comments

#484 - Track database/ITS1_DB.tsv instead of database/ITS1_DB.sql

Pull Request - State: closed - Opened by peterjc about 2 years ago - 6 comments

#483 - Track DB under version control, but not as SQL?

Issue - State: closed - Opened by peterjc about 2 years ago - 7 comments
Labels: question

#482 - Stricter right primer-trimming in w32 file?

Issue - State: closed - Opened by peterjc about 2 years ago - 2 comments

#481 - Extend partial NCBI refs with 32bp leader where observed - Part 2

Pull Request - State: closed - Opened by peterjc about 2 years ago

#480 - Extend partial NCBI references with 32bp leader where observed

Pull Request - State: closed - Opened by peterjc about 2 years ago - 3 comments

#479 - Document that we do see Phytophthora with differences in 32 leader

Issue - State: closed - Opened by peterjc about 2 years ago - 1 comment

#478 - Centralise the species name helper function

Pull Request - State: closed - Opened by peterjc about 2 years ago

#477 - Curating non-Phytophthora entries with missing 32bp leader?

Issue - State: closed - Opened by peterjc about 2 years ago - 11 comments
Labels: enhancement, question

#476 - Always show threshold and threshold-pool in summary reports

Pull Request - State: closed - Opened by peterjc about 2 years ago - 1 comment

#475 - Import via taxid in FASTA header

Pull Request - State: closed - Opened by peterjc about 2 years ago

#474 - Treat NCBI taxonomy merged.dmp like synonyms?

Issue - State: closed - Opened by peterjc about 2 years ago - 1 comment

#473 - replace usage of deprecated API

Pull Request - State: closed - Opened by maxbachmann about 2 years ago - 1 comment

#472 - Phytophthora sp. Kunnunara versus Kununurra?

Issue - State: open - Opened by peterjc about 2 years ago - 2 comments

#469 - Drop the human readable plain text summary report

Pull Request - State: closed - Opened by peterjc about 2 years ago - 2 comments

#468 - Drop human readable plain text sample report

Issue - State: closed - Opened by peterjc about 2 years ago - 1 comment

#457 - CI failing edit-graph test due to node name in networkx/pydot

Issue - State: closed - Opened by peterjc over 2 years ago - 4 comments
Labels: bug

#452 - Include undescribed species "Phytophthora taxon XXX" in curated set

Issue - State: closed - Opened by peterjc over 2 years ago - 2 comments
Labels: enhancement

#441 - Exporting unclassified sequences as FASTA file?

Issue - State: closed - Opened by peterjc over 2 years ago - 1 comment

#404 - Review treatment of species groups in NCBI taxonomy

Issue - State: open - Opened by peterjc almost 3 years ago - 1 comment
Labels: question

#402 - Compare examples all_reads intermediate TSV

Pull Request - State: closed - Opened by peterjc almost 3 years ago - 2 comments

#391 - Landa et al. (2021) ITS1 "British soil" as worked example

Pull Request - State: open - Opened by peterjc almost 3 years ago - 1 comment

#378 - Create github-actions.yml

Pull Request - State: open - Opened by peterjc about 3 years ago - 1 comment

#373 - References for (not using) metabarcoding quantification

Issue - State: open - Opened by peterjc about 3 years ago - 1 comment

#361 - Use cutadapt --no-indels?

Issue - State: open - Opened by peterjc about 3 years ago - 1 comment
Labels: question

#318 - References for synthetic controls

Issue - State: open - Opened by peterjc over 3 years ago - 3 comments

#261 - More report screenshots for documentation

Issue - State: closed - Opened by peterjc over 4 years ago - 3 comments

#221 - sample-summary table needs a TOTAL line

Issue - State: closed - Opened by peterjc almost 5 years ago - 3 comments
Labels: enhancement

#219 - Replace intermediate FASTA and TSV files with SQLite DB

Issue - State: closed - Opened by peterjc almost 5 years ago - 4 comments
Labels: enhancement

#151 - Include edit-graph in pipeline; --total default off

Pull Request - State: closed - Opened by peterjc over 5 years ago - 4 comments

#148 - Use joblib for doing Levenshtein edit dist in parallel

Pull Request - State: closed - Opened by peterjc over 5 years ago - 2 comments

#147 - edit-graph based PCR noise filter at plate or higher level

Issue - State: closed - Opened by peterjc over 5 years ago - 3 comments

#145 - compute edit-distances in parallel

Issue - State: closed - Opened by peterjc over 5 years ago - 1 comment
Labels: enhancement

#107 - Galaxy front end

Issue - State: open - Opened by peterjc over 5 years ago - 4 comments
Labels: enhancement

#105 - Two level classification: Species & Genus

Issue - State: open - Opened by peterjc over 5 years ago - 5 comments
Labels: enhancement

#39 - prepare-reads using dada2

Issue - State: open - Opened by peterjc almost 6 years ago - 2 comments
Labels: enhancement

#18 - Clustering database entries to flag taxonomic anomolies

Issue - State: open - Opened by peterjc almost 6 years ago - 22 comments

GitHub / peterjc/thapbi-pict issues and pull requests