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CHANGELOG.rst

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Changes for ya16sdb

0.8.2

  • Update to new NCBI assembly_summary_genbank.txt format
  • Other pipeline requirement updates

0.8.1

  • records are re-downloaded if their tax_ids have changed (GL: 100)

0.8.0

  • Switching to cmsearch from vsearch to filter non-16s sequences
  • New pipeline Dockerfile (GH: 41)
  • Basic length and ambiguity filtering for trusted type strains (GL: 89)
  • Dash app replaces match_species with type_classification (GH: 49)

0.7.3

  • Deduplicating WGS records by locus_tag (GL: 86)

0.7.2

  • Preferring same species in type strain match_species report (GH: 47)
  • Added SUCCESS or FAILED "at exit" of pipeline

0.7.1

  • Added "No Data" to ANI filters in Dash app
  • Added link to matching ANI assembly in Dash app table

0.7

  • Added ANI tax check annotations
  • Dependency updates
  • Cleaner pipeline
  • Cache files are consolidated into a hidden directory
  • All type strains are considered trusted unless part of do_not_trust list GL: 79
  • Bug fix to correct merge with vsearch nearest type strain GH: 39

0.6.1

  • Bug fix to include only records with updated taxids to be re-downloaded (GL: 72)

0.6

  • Sort and cap reference sequences by confidence (and other seq_info attributes) in blast db(s) (GL: 38)
  • Redownload records that have an updated modified_date to pick up changes in pubmed_id (GL: 17)
  • Do not re-download vsearch filtered sequences if training set has not been updated (GL: 44)
  • Move data/ignore.txt to /molmicro/lists dir and settings.conf and change file name to do_not_download.txt (GL: 47)
  • Include copy of /molmicro/common/uw/taxonomy/taxdmp.zip in dated output dir (GL: 48)
  • Update record tax_ids using accession2taxid from ncbi ftp site (GL: 54)
  • Create a "Trusted" list to compliment "Do Not Trust List" (GL: 57)

0.5

  • New dash based filter outlier plots (GL: 37)
  • Inclusion of tm7 Candidatus Saccharibacteria records (GL: 36)
  • Updated medirect to fix "Too Many Requests" issue with NCBI (GL: 42)
  • New api-key feature to increase the number of NCBI reqs/sec to 10 (GL: 43)

0.4

  • all paths (binaries, image locations, database credentials, etc) will be defined in a user defined file paths.conf (GH: 8, 9)
  • species only records to be paritioned (GH: 13)
  • new filtered/trusted/types directory (GH: 14)
  • new filtered/details_out.feather, [named, named/trusted, types, types/trusted]/lineages.[csv, txt] outputs (GH: 5)

0.3

  • new folder structure dedup -> 1200bp -> named -> filtered -> trusted

0.2

  • deduplicated refseq and original sequences, preferring the refseq sequence (GH: 20)
  • sequences determined obsolete by ncbi via esearch query are removed from database (GH: 13)
  • type strain sequences in filter_outliers plot will not align to themselves as nearest type strain (but might if another allele of itself is closest match) (GH: 29)
  • using JUST ncbi sequence_from_type filter to mark type strain sequences (GH: 14)

0.1

  • imported mkrefpkg SConstruct-ncbi