1.3.0 (2019-05-12)

  • pin biocommons dependencies to versions that support 2.7 and 3.5+ [25bc21f]

Changes since 1.2.5.post1 (2019-02-01).

Bug Fixes

  • Fixes #474, fixes #492: correct for stop gain located at termination codon (#518)
  • Fixes #501: Add c_to_p support for inversion (#502)

New Features

  • Closes #243: implement hgvs-to-vcf translation
  • Closes #499: recognize whole-gene dup (c.-i_*j) and assume does not affect protein sequence [dc48d5d]
  • Closes #511: Update misc/experimental/vcf-add-hgvs to support newer bioutils and pyvcf [88e01d4]
  • Closes #257: Support parsing gene names and optional addition during projection
  • Closes #557: Add option to format translation initiation codon variants as p.Met1?

p.Met1? is the new default [2cd86b9] * Added parse shorthand for parse_hgvs_variant [69c2aeb] * Added t_to_p in AssemblyMapper [8f9b69b] * hgvs.easy: Provide single-file import with usable defaults and functional forms for common commands (#516) * Updated hgvs-guess-plausible-transcripts [4e2a9d0] * Updated default uta to uta_20180821 [e8206d1]

Internal, Developer, and Experimental Changes

  • Closes #544: Update installation docs [ae3064c]
  • Closes #500: unpinned setuptools_scm [bae7e4a]
  • Closes #494: Removed useless warning (Closing connection; future mapping and validation will fail) [dfa0c52]
  • Added Python syntax highlighting (#550)
  • Added doctests for hgvs/utils/norm.py (#548)
  • Expose seqrepo reference in SeqFetcher instance [3ab49e9]
  • Fix typo in docs (#554) [5b25b4f]
  • When re-raising exception from sequencing fetching, including fetcher implementation and underlying exception message [42859e4]
  • add 3.7 support to Makefile [3a89a82]
  • added link to hgvs notebooks on mybinder.org [3077d3c]
  • added notebook of hdp output examples [4fb9617]
  • don’t warn about pickle.load() [f052d03]
  • emit CRITICAL log message on Python < 3.6 [b7f320a]
  • expose seqrepo reference in SeqFetcher instance [3ab49e9]
  • fix regexp that didn’t use a raw (r””) string (DeepSource) [f6126f6]
  • fix: expected results in quick_start.rst doctest were unsorted [63d5e74]
  • fixed incompatibilities with newer version of pytest [ee9426f]
  • fixed redundant exception imports (DeepSource) [dc6277d]
  • minor code cleanup based on pylint testing [927864d]
  • ooops… used f string in 2.7 version :-( [5c3492a]
  • remove del sequence from variants being tested (and remove re module DeprecationWarnings); and fix latent bugs in tests [2cb053d]
  • remove relative path in pkg_resources.resource_filename() to eliminate warning about future failure [19a16d5]
  • updated pytest mark configuration [d922495]