Changes since 0.3.7 (2015-06-23). See issues at milestone 0.4.0.
- #227: x_to_r and r_to_x methods were renamed to x_to_n and n_to_x as part of support for non-coding transcripts.
- #231: The UTA data provider will use a recently updated database by default (uta_20150827). Clients with custom configurations should use postgresql://anonymous:email@example.com/uta/uta_20150827. (Note the change of hostname, username, and password as well; see Deprecations.)
- #238: Most methods now raise HGVSDataNotAvailableError when expected data is not available. Previously, None was returned for some methods.
- #244: Removed cache_transcripts argument from VariantMapper. This argument was deprecated in 0.3.0 and is now obsolete. Dataproviders are now expected to cache data.
- #246: Remove hgvsX_to_hgvsY methods. These methods were deprecated in 0.3.0 and are now obsolete.
- #247: Dup and Repeat “seq” instance variable renamed to “ref” for consistency.
- EasyVariantMapper, Normalizer, and Validator now fetch sequence data at runtime, which may raise performance and privacy concerns. Users may wish to read Privacy Issues in the documentation.
- UTA: UTA now uses anonymous:anonymous as the username:password. uta_public:uta_public will be obsolete shortly.
- #44: Added variant normalization and use during mapping. Thanks to Meng Wang and Kevin Jacobs for contributions. (pull request #17)
- #168: EasyVariantMapper supports replacing the reference sequence during mapping and enabled by default.
- #227: Implement initial support for non-coding transcripts.
- #230: Allow full IUPAC for NA and AA, with tests. Previously, the grammar admitted only ACGTU.
- #233: Added get_similar_transcripts() to data UTA provider to expose UTA’s tx_similarity view.
- #234, #241: Preferentially use transcript-protein accession associations from RefSeq when mapping c. to p. variants. Previously, when multiple protein accessions were associated with a single distinct sequence, the p. accession was arbitrary.
- #236, #240: Added seqfetcher.SeqFetcher to fetch sequences from NCBI & Ensembl
- #250: Implemented configuration module; hgvs.global_config is initialized once and available globally
- #251: Parens now optional around p. edits; default is enabled per HGVS spec (hgvs.global_config.mapping.inferred_p_is_uncertain)
- #255: variants normalized by EasyVariantMapper by default [BROKEN: 1b85d4deabc3]
- #261: Replace reference default from config (hgvs.global_config.mapping.replace_reference)
- UTA is now available as a docker image for local installation. See Local Installation of UTA.
- #213: Clarify warning message when validating intronic variants.
- #254: Support inversion, conversion, and nadupn variants
- Added misc/experimental/tx-seq-discrepancies to identify genomic locations of reference-transcript discrepancies
- Added variant context method to evm (temporary location, but useful for debugging)
- HGVSInternalError now subclasses HGVSError (not Exception) [BROKEN: ff6cd4dc51dc]
- Lots of documentation updates.
- Raise HGVSParserError (instead of ometa.runtime.ParseError) when parsing fails [BROKEN: efa93fe29d15]
- The UTA data provider now checks for the requested schema on connection and provides more informative errors on failure.
- hdp.data_version returns schema name for UTA since that that is the conventional use.
- Use autocommit to prevent transaction overhead and locks [BROKEN: 65d69e41716e]
Internal and Developer Changes¶
- #263: Trying out a new tag-based changelog mechanism for 0.4.0 and 0.4 series.
- All code will be mercilously reformmated with yapf occasionally using .style.yapf
- Build and upload wheel packages (in addition to existing eggs and tarballs)
- Docs significantly overhauled and moved to readthedocs.org with automatic webhook-based building
- Enable users to set application_name when connecting [BROKEN: 835ac7771909]
- _UTA_URL_KEY (dev use only) will switch URLs to any in hgvs/_data/defaults.ini
- on import of hgvs, emit logging info line w/version [BROKEN: aa97f2c1cdc8]
- sped up most tests by using setUpClass() rather than setUp() [BROKEN: a6d227f6a3e0]