snps - v2.9.0

What's Changed

• Fix linting issues by @apriha in https://github.com/apriha/snps/pull/179
• Parse Sano DTC format by @apriha in https://github.com/apriha/snps/pull/180
• Add support to detect plink generated 23andme files by @teepean in https://github.com/apriha/snps/pull/176
• Add PLINK test by @apriha in https://github.com/apriha/snps/pull/181
• Parse PLINK by @apriha in https://github.com/apriha/snps/pull/182
• Fix DtypeWarning by @apriha in https://github.com/apriha/snps/pull/183
• Enhance VCF output by @apriha in https://github.com/apriha/snps/pull/184

New Contributors

• @teepean made their first contribution in https://github.com/apriha/snps/pull/176

Full Changelog: https://github.com/apriha/snps/compare/v2.8.2...v2.9.0

- Python
Published by apriha over 1 year ago

snps - v2.8.2

What's Changed

• Lint and format with Ruff by @apriha in https://github.com/apriha/snps/pull/175
• Fix OverflowError by @apriha in https://github.com/apriha/snps/pull/178

Full Changelog: https://github.com/apriha/snps/compare/v2.8.1...v2.8.2

- Python
Published by apriha over 1 year ago

snps - v2.8.1

What's Changed

• CI updates by @apriha in https://github.com/apriha/snps/pull/172
• Fix GenomePrep resources by @apriha in https://github.com/apriha/snps/pull/174

Full Changelog: https://github.com/apriha/snps/compare/v2.8.0...v2.8.1

- Python
Published by apriha almost 2 years ago

snps - v2.8.0

What's Changed

• Fix CI issues by @apriha in https://github.com/apriha/snps/pull/169
• Support modern Python versions by @apriha in https://github.com/apriha/snps/pull/170
• Update ezancestry, works local by @arvkevi in https://github.com/apriha/snps/pull/171

Full Changelog: https://github.com/apriha/snps/compare/v2.7.2...v2.8.0

- Python
Published by apriha almost 2 years ago

snps - v2.7.2

Updated

• Fix CI builds

- Python
Published by apriha almost 3 years ago

snps - v2.7.1

Updated

• Fix CI builds

- Python
Published by apriha about 3 years ago

snps - v2.7.0

Added

• Detect deduced chip array and chip version based on chip clusters
• Identify and filter low quality SNPs based on chip clusters
• Add various VCF output options related to low quality SNPs (drop and/or populate FILTER column)
• Add helper output functions (to_csv, to_tsv, to_vcf)
• Add ability to prefix chromosomes in VCF output

Updated

• Deprecate reading/writing class methods
• Deprecate save method

Fixed

• Write output file with no additional blank lines (Windows)

- Python
Published by apriha over 3 years ago

snps - v2.6.0

Added

• Add support for CircleDNA
• Enable specification of unavailable VCF ALT allele

Updated

• More robust parsing of AncestryDNA and 23andMe files

- Python
Published by apriha over 3 years ago

snps - v2.5.0

Added

• Add support for Python 3.10

- Python
Published by apriha over 3 years ago

snps - v2.4.4

Updated

• Fix CI builds

- Python
Published by apriha over 3 years ago

snps - v2.4.3

Updated

• Fix CI builds

- Python
Published by apriha almost 4 years ago

snps - v2.4.2

Updated

• Fix CI builds
• Update banner

- Python
Published by apriha about 4 years ago

snps - v2.4.1

Updated

• Configure Read the Docs builds

- Python
Published by apriha over 4 years ago

snps - v2.4.0

Added

• Add ancestry prediction capability via ezancestry (#143)

Updated

• Support current version of black (#144)

- Python
Published by apriha over 4 years ago

snps - v2.3.0

Added

• Add binary output buffer support (#139)

Updated

• Change minimum supported Python version (#140)

- Python
Published by apriha over 4 years ago

snps - v2.2.0

Added

• Implement __len__

Updated

• Improve and expand build detection
• Improve and refactor several readers (#133, #136)
• Allow specification of sex detection method for allele deduplication
• Refactor remapping code

Fixed

• Fix build detection
• Fix race condition when downloading resources

- Python
Published by apriha over 4 years ago

snps - v2.1.4

Updated

• Make REST calls more robust (#131)
• Make output of __repr__ more succinct
• Use stable build for docs

- Python
Published by apriha over 4 years ago

snps - v2.1.3

Updated

• Parallelize writing VCF
• Use temp dir for output files during tests (#99)

- Python
Published by apriha almost 5 years ago

snps - v2.1.2

Updated

• Setup GitHub Actions
• Fix tests on macOS and Windows

- Python
Published by apriha almost 5 years ago

snps - v2.1.1

Updated

• Improve VCF parsing (#118)
• Improve usability of Reader and Writer classes (#115)

- Python
Published by apriha about 5 years ago

snps - v2.1.0

Added

• Add support for Python 3.9
• Add chrom parameter to SNPs.merge

Updated

• Use set for rsids
• Simplify parsing Ancestry files

- Python
Published by apriha over 5 years ago

snps - v2.0.3

Updated

• Update URL for Ensembl REST API

- Python
Published by apriha over 5 years ago

snps - v2.0.2

Updated

• Make chromosome-based lookups faster
• Use f-strings for string formatting (#100)
• Documentation updates

- Python
Published by apriha over 5 years ago

snps - v2.0.1

Updated

• Support additional Mapmygenome header (#94)

- Python
Published by apriha over 5 years ago

snps - v2.0.0

Added

• Add support for tellmeGen files
• Add SNPs.merge method (#88)
• Remap SNPs as necessary during merge
• Return results for each merge (e.g., SNPs in common)
• Deduplicate MT chromosome alleles (#65)
• Add documentation for normalized snps dataframe
• Identify discrepant SNPs when saving VCF

Updated

• Change minimum supported Python version (#64)
• Change default separator to tab (#66)
• Change default value for assign_par_snps
• Enhance build detection
• Obsolete SNPsCollection object (#88)
• Rename several SNPs methods and properties (#92)
• Refactor normalized snps dataframe with np.uint32 dtype for pos
• Update examples and documentation

- Python
Published by apriha over 5 years ago

snps - v1.2.3

Fixed

• Fix build issues

- Python
Published by apriha over 5 years ago

snps - v1.2.2

Fixed

• Fix issue building docs

- Python
Published by apriha over 5 years ago

snps - v1.2.1

Fixed

• Assign PAR SNPs before deduplicating XY chroms

Updated

• Enhance documentation

- Python
Published by apriha over 5 years ago

snps - v1.2.0

Added

• Add support for parsing a variety of generic files
• Add scripts to parse files in the openSNP datadump

Updated

• Enhance build detection (#6)
• Handle several types of parsing issues
• Handle download exceptions
• Perform minimal downloads during tests
• Refactor classes to files
• Improve tests to read various combinations of inputs

Fixed

• Fixed several minor bugs through added testing

- Python
Published by apriha over 5 years ago

snps - v1.1.1

Fixed

• Fix Travis CI build script

- Python
Published by apriha almost 6 years ago

snps - v1.1.0

Added

• Add support for DNA.Land files

- Python
Published by apriha about 6 years ago

snps - v1.0.2

Fixed

• Fix error when saving a VCF with no SNPs (#57)
• Log when no SNPs are loaded (#57)
• Pin version of pandas (#59)

- Python
Published by apriha about 6 years ago

snps - v1.0.1

Fixed

• Handle merged RSIDs when assigning PAR SNPs
• Read tab-separated files generated by snps

- Python
Published by apriha about 6 years ago

snps - v1.0.0

Added

• Add phased property
• Add ability to de-duplicate RSIDs
• Add ability to de-duplicate non-PAR X and Y chromosome alleles for males
• Add openSNP datadump resource
• Add methods to get heterozygous SNPs and not null SNPs
• Add parameter to count SNPs on a chromosome
• Add ability to determine sex using X or Y chromosome methods

Updated

• Update thresholds for determine_sex based on analysis of openSNP data
• Refactor parsing
• Fix NA values for Sano Genetics files

- Python
Published by apriha about 6 years ago

snps - v0.7.0

Added

• Add support for Sano Genetics files

Updated

• Improve reading and parsing of files
• Update resources for Global Screening Array

- Python
Published by apriha about 6 years ago

snps - v0.6.2

Updated

• Refactor exception handling (#38)
• Update documentation

- Python
Published by apriha over 6 years ago

snps - v0.6.1

Updated

• Update CONTRIBUTING.rst
• Update log levels
• Make save_snps parameters consistent

- Python
Published by apriha over 6 years ago

snps - v0.6.0

Added

• Parse large VCF files (optionally compressed with gzip)
• Extract a list of RSIDs from a VCF
• Add SNPs.unannotated_vcf property
• Add documentation for reading VCF (#18)

Updated

• Improve speed of reading VCF files (#11)
• Replace print statements with calls to a logger (#22)
• Do not drop chromosome 0 SNPs
• Install additional dev dependencies with Pipenv
• Fix warnings when generating documentation
• Update tests and documentation

- Python
Published by apriha over 6 years ago

snps - v0.5.0

Added

• Add support for Mapmygenome files
• Add support for Python 3.8

- Python
Published by apriha over 6 years ago

snps - v0.4.0

Added

• Add support for Código 46 files
• Add support for LivingDNA files

- Python
Published by apriha over 6 years ago

snps - v0.3.0

Added

• Read and write streams (#16)
• Add capability to only detect source of SNPs

Updated

• Update SNPs banner

- Python
Published by apriha over 6 years ago

snps - v0.2.1

Updated

• Update URL for GRCh37 reference sequences

- Python
Published by apriha over 6 years ago

snps - v0.2.0

Added

• Add support for Genes for Good files

- Python
Published by apriha over 6 years ago

snps - v0.1.1

Updated

• Minor testing and documentation updates

- Python
Published by apriha over 6 years ago

snps - v0.1.0

Start snps package with capability developed on lineage

- Python
Published by apriha over 6 years ago