Recent Releases of lineage
lineage - v4.4.0
What's Changed
- Fix CI issues by @apriha in https://github.com/apriha/lineage/pull/111
- Support modern Python versions by @apriha in https://github.com/apriha/lineage/pull/112
- CI updates by @apriha in https://github.com/apriha/lineage/pull/113
Full Changelog: https://github.com/apriha/lineage/compare/v4.3.1...v4.4.0
- Python
Published by apriha almost 2 years ago
lineage - v4.1.3
Updated
- Change minimum supported Python version
- Support current version of
black - Configure Read the Docs builds
- Python
Published by apriha about 4 years ago
lineage - v4.1.0
Added
- Add support for 1000 Genomes Project genetic maps (#23)
Updated
- Mock downloads during tests
- Update documentation
- Python
Published by apriha almost 5 years ago
lineage - v3.1.0
Added
- Add support for Python 3.8
Updated
- Fix warnings when generating documentation
- Install additional dev dependencies with Pipenv
- Update tests and documentation
- Update
get_all_resourcesto only downloadlineageresources - Replace print statements with calls to a logger (#71)
- Refactor exception handling
- Python
Published by apriha over 6 years ago
lineage - v3.0.0
Added
- Find shared DNA between an arbitrary number of individuals
- Return discrepant SNPs discovered while finding shared DNA
- Add support for VCF files
Updated
- Refactor
lineage.snpsassnpspackage - Move
Lineage.remap_snpstoSNPs.remap_snps - Output results of
find_shared_dnaas a dict - Ensure types are consistent
- Update CSV header
- Update default for
parallelizeparameters
- Python
Published by apriha over 6 years ago
lineage - v2.0.0
Added
- Write files atomically
- Add support for MyHeritage files
- Parallelize remapping SNPs
Updated
- Refactor using inheritance
- Fix deprecations
- Utilize functional programming
- Python
Published by apriha almost 7 years ago
lineage - v1.1.1
Updated
- Improve testing
- Re-structure library using cookiecutter-pylibrary
- Python
Published by apriha almost 7 years ago
lineage - v1.1.0
Start versioning with Semantic Versioning.
Added
- Add support for FTDNA "famfinder" filetype
- Add SNP to
detect_build
Updated
- Reformat code with Black
- Decrease margins on shared DNA plots
- Python
Published by apriha almost 7 years ago
lineage - v1.0.3
Added
- Add ability to turn on / off all file output
- Add
discrepant_snpsproperty toIndividual - Add helper methods to
SNPsclass
Updated
- Return
pandas.DataFrameobjects fromfind_shared_dna - Include assembly in filenames of output files
- Include header comments in all output files
- Update documentation
- Python
Published by apriha about 7 years ago
lineage - v1.0
Added
- Add
SNPsclass - Add summary properties to
SNPsandIndividual - Incorporate HapMap PAR regions / find shared DNA in PAR regions
- Assign PAR SNPs to the X or Y chromosome
- Determine sex based on X and Y chromosome SNPs
- Cache assembly mapping data
- Add ability to download all resources
- Add header to output file generated when saving SNPs
- Add support for Python 3.7
Updated
- Improve processing of X chromosome / PAR regions
- Handle SNPs not remapped
- Return discrepant SNPs when loading files
- Pin requirements
- Update tests
- Python
Published by apriha over 7 years ago
lineage - v1.0b3
Added
- Add tests and integrate with Codecov
- Integrate with Read the Docs
- Add banner and badges
Updated
- Return results from various functions
- Fix some bugs
- Python
Published by apriha almost 8 years ago
lineage - v1.0b2
Added
- Detect assembly of SNPs being loaded
- Automatically remap SNPs to Build 37 for processing (if necessary)
Updated
- Simplify the interface for remapping SNPs
- Use the The Versioneer for versioning
Removed
- Remove support for processing with Build 36 (remap SNPs to Build 37 instead)
- Python
Published by apriha about 8 years ago
lineage - v1.0b1
Added
- Merge raw data files from different DNA testing companies, identifying discrepant SNPs in the process
- Compute centiMorgans (cMs) of shared DNA between individuals using HapMap tables
- Plot shared DNA between individuals
- Determine genes shared between individuals (i.e., genes transcribed from shared DNA segments)
- Remap SNPs between assemblies / builds (e.g., convert SNPs from build 36 to build 37, etc.)
- Download example datasets from openSNP
Updated
- Find discordant SNPs between child and parent(s)
- Python
Published by apriha over 8 years ago