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CHANGES.md

v0.3.0-alpha

  • major changes to the command-line API
    • the new API now uses a subcommand system: pyani <cmd> <arguments>
  • major changes to result storage
    • results are now stored in an SQLite database, rather than reported to .tab files
    • enables reuse of previously calculated results in new analyses
    • enables generation of multiple output files from the same analysis, after the analysis is complete
  • more output formats
    • tabular output is available as HTML tables, as well as plain text
  • new documentation
    • documentation is now available at ReadTheDocs
    • papers citing or referring to pyani are now listed
  • pyani download (replacing genbank_get_genomes_by_taxon.py) allows use of an NCBI API key for faster/more stable downloads
    • genbank_get_genomes_by_taxon.py label/class file output updated to include a hash, matching the pyani download output format
  • pyani plot now produces distribution plots in addition to heatmaps
  • A number of bug fixes were implemented, including:
    • consistent handling of filenames as Paths
    • alignment length calculation for ANIm was corrected
  • major refactoring of code ported from v0.2
    • static typing implemented
  • testing converted to pytest conventions from unittest

v0.2.7.dev

  • update legacy BLAST download location in TravisCI
  • update concordance tests (issue #105)
  • extend test suites (issue #104)
  • modify ANIm concordance test to accommodate new command structure
  • add delta-filter wrapper for compatibility with SGE/OGE schedulers

v0.2.7

  • Fix for issue #97 where numeric arguments to the GenBank download script were not recognised
  • GenBank download script now insists on integer input for --batchsize, --retries, and --timeout
  • Added setup.cfg that points to README.md
  • Fix issue #97 where valid input arguments were not recognised in the download script

v0.2.6

  • Add Dockerfiles for making Docker images

v0.2.4

  • ANIm now uses delta-filter to remove alignments of repeat regions (issue #91)
  • added --filter_exe option to specify location of delta-filter utility (issue #91)
  • fixed --format option so that GenBank downloads work again (issue #89)
  • add --SGEargs option to average_nucleotide_identity.py for custom qsub settings
  • README.md badges now clickable
  • --version switch added to average_nucleotide_identity.py
  • FTP timeouts are now caught differently in genbank_get_genomes_by_taxon.py
  • Additional characters in NCBI FTP URIs now escaped in genbank_get_genomes_by_taxon.py - should be fewer failed downloads
  • Modified error messaging when NUCmer alignment fails
  • average_nucleotide_identity.py argument documentation improvements
  • Script now fails immediately if label or class files missing (issue #78)
  • Changes to --noclobber log behaviour (issue #79)
  • fixed --rerender code (issue #85)

v0.2.3

  • fixes a bug in the installed scripts where the shebang (#!) in wheel and egg packages pointed to a development Python

v0.2.2

  • fix for issue #53 (--maxmatch has no effect)
  • fix to genbank_get_genomes_by_taxon.py to account for NCBI FTP location changes
  • fixed issue #52 (local variable bug)
  • fixed issued #49 (TETRA failure) and #51 (matplotlib bug)
  • add several tests and support for codecov.io, landscape.io and Travis-CI
  • removed requirement for rpy2
  • moved scripts to bin/ subdirectory

v0.2.1

  • pyani now requires rpy2 v2.8.0 in order to satisfy running under Anaconda (see issue #26)
  • pyani now checks for presence of rpy2 and - when run from source - if rpy2 is not available, pyani doesn't throw an error until R graphical output is requested. If installed -via- pip, then pyani still raises pkg_resources.DistributionNotFound if rpy2 is missing.
  • Updated genbank_get_genomes_by_taxon.py script to use the new FTP locations at NCBI for each assembly.
  • Fixed bug where ANIb would not go to completion if empty BLASTN files were generated (see issue #27)
  • Fixed bug where ANIm would not finish under multiprocessing if input sequences were highly divergent.
  • Added Hadamard product of percentage identity and alignment coverage as output.
  • Fixed bug where label/classes are out of sync with new NCBI downloaded filenames
  • Added --rerender option to draw (new) graphics from old output, without recalculation
  • Corrected matplotlib row dendrogram orientation
  • Seaborn output no longer dumps core on large (ca. 500 genome) datasets
  • genbank_get_genomes_by_taxon.py attempts to identify cause for failed downloads and correct, where nomenclature/versions are at fault
  • graceful replacement of classes that are not present in classes.txt
  • add pyani version to log file

v0.2.0

  • Merged pull request from peterjc to make printing from tests Python3-friendly.
  • Merged pull request from peterjc to use open() for opening files.
  • Merged pull request from peterjc to cope with missing labels/classes more gracefully
  • Fixed -s/--fragsize option in average_nucleotide_identity.py (thanks to Joseph Adelskov for hte report).
  • BLAST and nucmer results are now written to a subdirectory of the output folder. By default, these sequence search output files are compressed, but this behaviour can be suppressed using the --nocompress option.
  • Added genbank_get_genomes_by_taxon.py as an aid to downloading publicly-available genome files from GenBank, for analysis.