sierra-local - Version 0.4

• deprecated subtyper.py script, subtyping is no longer supported
• handle ambiguous codons (#72)
• added reference/ genotype update scripts (b4a1fc0)
• bug fixes (#92, #99)

Scientific Software - Peer-reviewed - Python
Published by ArtPoon about 2 years ago

sierra-local - Version 0.3

What's Changed

• Use submodule to retrieve data files by @GopiGugan in https://github.com/PoonLab/sierra-local/pull/68
• Update dev branch with recent changes by @GopiGugan in https://github.com/PoonLab/sierra-local/pull/78
• Adding Postalign as Alignment Program by @WilliamZekaiWang in https://github.com/PoonLab/sierra-local/pull/83
• Switch to postalign and updating unit tests, resources by @ArtPoon in https://github.com/PoonLab/sierra-local/pull/82
• Adding subtyping option and fixes to -json by @WilliamZekaiWang in https://github.com/PoonLab/sierra-local/pull/86
• Updating Post-align Dependencies by @WilliamZekaiWang in https://github.com/PoonLab/sierra-local/pull/88

New Contributors

• @GopiGugan made their first contribution in https://github.com/PoonLab/sierra-local/pull/68
• @WilliamZekaiWang made their first contribution in https://github.com/PoonLab/sierra-local/pull/83

Full Changelog: https://github.com/PoonLab/sierra-local/compare/v0.2.1...v0.3

Scientific Software - Peer-reviewed - Python
Published by ArtPoon almost 3 years ago

sierra-local - Version 0.2.1

Bug fix

Scientific Software - Peer-reviewed - Python
Published by ArtPoon almost 7 years ago

sierra-local - Version 0.2.0

The updater.py script is now deprecated due to changes in the HIVdb website.

Scientific Software - Peer-reviewed - Python
Published by ArtPoon almost 7 years ago

sierra-local - Re-release of v0.1.2 for JOSS

• Added CONTRIBUTING.md file
• Added /paper containing manuscript files for submission to JOSS

Scientific Software - Peer-reviewed - Python
Published by ArtPoon over 7 years ago

sierra-local - v0.1.2

• package includes NucAmino binaries
• fixed subtyping
• parsing JSON output from NucAmino to address full-length pol issue
• writes temporary alignment file to screen for illegal characters
• separating alignment data by gene
• wrote detailed installation instructions

Scientific Software - Peer-reviewed - Python
Published by ArtPoon over 7 years ago

sierra-local -

• ported HIV subtyping from HIVdb pipeline
• setup script sets user permissions for system installation to allow users to access downloaded resources
• moved gui.py to a separate branch as a work in progress
• extensive refactoring and application of PEP8 code style
• byte string conversion to accommodate Python 3.5
• moved FASTA parsing to utils.py
• fixes #44, #42

Scientific Software - Peer-reviewed - Python
Published by ArtPoon over 7 years ago