CHANGELOG.md

Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

[Unreleased]

Added

• A relax option to fidibus to proceed with prep task despite failed shasum verification.
• The *.protein2ilocus.repr.tsv file containing mapping for iLocus representatives only.
• Better exception handling/reporting for failed downloads.
• Reference genome configurations for Zootermopsis nevadensis (in support of the BWASP project) and Orchesella cincta (as additional proof-of-concept).
• Support for all Genbank genomes, not just those within RefSeq.
• Restored support for HymenopteraBase versions of several ant genomes.

Changed

• Ancillary files .ilocus.mrnas.txt and .protein2ilocus.txt are not .tsv files with headers.
• Extensive documentation updates.
• Switched from nose to py.test as the testing framework.
• Updated checksums for many NCBI annotations to compensate for, among other things:
  • changes in ##species pragmas
  • transcript evidence descriptions and other metadata
  • feature types for annotated mobile elements, antisense transcripts, origins of replication, and various other features
  • an update to the C. elegans annotation (< 1% gene models affected)
  • an update to the D. rerio annotation (≈ 3% CDS exons, ≈ 10% all exons affected)
  • an update to the M. musculus annotation (1% CDS exons, 5% of all exons affected)

Removed

• Deprecated genhub-fix-trna.py script.

[0.4.0] - 2016-05-09

Changed

• The genhub-build.py script is now fidibus, and the CLI was updated.
• Pdom, Pcan, and Dqua now default to RefSeq genomes, with Toth Lab and CRG genomes available under labels Pdtl, Pccr, and Dqcr.

Fixed

• The cluster build task now uses -M 0 by default.
• The Registry class was simplified.

Added

• The build script (now fidibus) now has support for custom genomes.
• Sequence IDs are now reported for iLocus and miLocus tables.
• New script for creating a piLocus summary table.
• Recipes for chick pea, cabbage, and soybean.
• Recipes for another mosquito (Aedes aegypti) and a spider mite (non-insect arthropod).
• A --shuffled option to several scripts for reading from *iloci.shuffled.tsv, and improved access from the GenomeDB class.

[0.3.7] - 2016-03-19

Fixed

• Correctly included missing script in setup.py.

[0.3.6] - 2016-03-19

Added

• New recipe for cotton.
• New recipe for Daphnia pulex.
• New script for creating an iLocus summary table.

[0.3.5] - 2016-03-17

Fixed

• Updated test data files to compensate for corrections to LocusPocus' reporting of iLocus type.

[0.3.4] - 2016-03-16

Added

• Added seqfilter to RefSeq module and .yaml configs.

Fixed

• Used new seqfilter mechanism to eliminate redundant patch and variant data from human and mouse genomes.
• Updated rice recipe following an update to the corresponding RefSeq entry.

[0.3.3] - 2016-03-03

Fixed

• Filled out partial implementation of --delta option for the build script.

[0.3.2] - 2016-03-02

Fixed

• Removed gene model with overlapping exons causing processing issues in C. reinhardtii.

[0.3.1] - 2016-02-24

Fixed

• Removed unnecessary Fragment column from .iloci.tsv table. Redundant with LocusClass=fiLocus.
• Removed outdated code for computing LocusClass.
• Fixed feature for specifying iLocus label format.

[0.3.0] - 2016-02-24

Added

• Integration with codecov.io.
• Lots of genome recipes
  • Anopheles gambiae
  • Homo sapiens
  • Theobroma cacao
  • some version-specific recipes
    • TAIR6
    • Apis mellifera assembly 2.0 / OGS 1.0
    • Apis mellifera assembly 4.5 / OGS 3.2
  • 9 species of green algae
• Implemented the cleanup and cluster tasks for the main build script.

Changed

• Unit test fixtures to account for AEGeAn's improved reporting of iLocus types.
• Protein checksum for Xenopus tropicals, which was recently updated to drop the Silurana designation.

[0.2.1] - 2016-01-15

Fixed

• versioneer issue with MANIFEST

[0.2.0] - 2016-01-15

Added

• Recipe for the rice genome (Oryza sativa L. ssp. japonica).
• Recipe for a model legume genome (Medicago truncatula).
• Batch for all Hymenoptera.
• Multiprocessing support for build script.

Changed

• Complete overhaul of the genome configuration handling (now in the registry module).
• Minor changes to the Travis CI configuration.
• Excluded Danio rerio config from CI tests, as its resource requirements are right at the limit of what the Travis VMs can handle.
• Updated Xenopus tropicalis config to drop the parentheses in the species name.
• Updated Drosophila melanogaster config to the latest RefSeq assembly/annotation.
• Moved sha1 and file resolution code from __init__.py to GenomeDB class.

[0.1.2] - 2016-01-09

Added

• Package metadata.

Fixed

• Minor improvements to documentation.

[0.1.1] - 2016-01-08

Fixed

• Added pre-requisites to setup.py.

[0.1.0] - 2016-01-08

Added

• first stable release!
• GenomeDB class and various extensions for downloading and formatting data.
• Modules for parsing and describing iLoci, proteins, mRNAs, exons, introns, and coding sequences.
• The script implementing the stats task, brought over with minimal changes from HymHub.
• Unit tests, with 100% success rate and 100% coverage of core package code (not scripts yet).
• Minimal installation and usage documentation.