Skip to content

Latest commit

 

History

History
137 lines (101 loc) · 3.97 KB

CHANGES.rst

File metadata and controls

137 lines (101 loc) · 3.97 KB
Raw

Changes for deenurp

0.3.2

  • Dependency updates and Python3 conversion bug fixes

0.3.1

  • building Docker image and test casese using Github Actions

0.3.0

  • Python 3 support and other dependency upgrades and bug fixes

0.2.7

  • removed peasel requirement

0.2.6

  • filter_outliers performance improvements

0.2.5

  • new deenurp filter_outliers --no-filter list of taxids argument [GH-65]
  • fixed some Python Pandas warnings (GH: 50)
  • fix error when query and reference sequences have name collision

0.2.4

  • update infernal to 1.1.2
  • install cmsearch and cmcalibrate
  • update taxtastic to 0.8.5
  • update versions of various other dependencies

0.2.3

  • add seqmagick to requirements.txt
  • create moinpoints in Docker image

0.2.2

  • fix version number in docker and singularity containers

0.2.1

  • bugfix: fix error parsing cmalign scores file
  • add Singularity build instructions

0.2.0

  • add subcommand 'dereplicate_named'
  • add new clustering method to filter_outliers (--cluster-type RobustSingleLinkage)
  • update defaults for filter_outliers
  • use vsearch 2.5.0
  • fix error in fill_lonely raised by node with no parent
  • added deenurp orientate_sequences --out_notmatched_taxids
  • address edge case in select_references which too few refs representing a species remain after clustering at CLUSTER_THRESHOLD
  • remove subcommand tax2tree (along with dependencies on t2t and cogent)
  • remove subcommand rdp_extract_genbank
  • add Dockerfile (thanks, Sam Minot!)
  • update many dependencies

0.1.8

  • deenurp ncbi_extract_genbank will die after 10 query retries

0.1.7

  • replace uclust with vsearch (uclust dropped as dependency)
  • bootstrap.sh installs python requirements in specified order with --no-deps
  • installs vsearch 1.10.2

0.1.3

  • bumping pplacer support to v1.1.alpha17
  • adding pandas support to versions 0.17.*
  • deenurp orientate_sequences takes a training set (data/types.fasta) and aligns sequences reverse complementing when necessary (GH-34)
  • travis caching is setup for pip installs (GH-22)
  • fixed pep 440 versioning bug when installing and running unittests (GH-31)
  • new deenurp select-references --include-clusters --exclude-clusters --exclude-sequences arguments
  • new deenurp fill_lonely --include-taxid --exclude-taxid arguments

0.1.2

  • deenurp rdp_extract_sequences now updates old tax_ids instead of dropping them (GH-27)
  • deenurp rdp_extract_sequences creates new column taxid_classified instead of dropping tax_ids of unclassified sequences (GH-28)
  • function tax_of_genbank no longer returns None if string 'uncultured bacterium' is in the organism name (GH-29)
  • expanding type strain designations to include more terms (GH-16)

0.1.1

  • gb2csv creates a csv of Genbank records and optionally the references (GH-23)
  • using new container based Travis build (GH-24)

0.1.0

  • filter-outliers can calculate pairwise distances using cmalign, muscle, or vsearch
  • filter-outliers can use hierarchical clustering for outlier detection (--strategy cluster)
  • output of filter-outliers --detailed-seqinfo includes centroid, distance from centroid, etc
  • add dependencies on pandas, scipy, and scikit-learn
  • bootstrap script installs muscle and vsearch
  • add subcommand deenurp pairwise-distances
  • version number defined using git describe --tags --dirty

0.0.3

  • deenurp search-sequences learned option --search-threshold to allow more permissive database searches
  • Suppress FastTree messages in the absence of an error

0.0.2