dammit v1.2

Fixes several major bugs / introduces improvements:
- updates TransDecoder and HMMER parsing for TransDecoder 5 (the "query_name" KeyError)
- uses peptide coordinates from longest_orfs.pep for remapping and introduces parser for it
- forces TransDecoder v5
- updates the MafParser to support erroneously inserted newlines (seems to show up against sprot)

Zenodo Handle

Handle for zenodo DOI.

v1.1

new functionality:

• add --no-rename option, which allows you to keep original transcript names
• add swissprot mapping to default pipeline
• patch NR pipeline
• new home (dib-lab) for repo & docs

release contributors:
@camillescott, @bluegenes, @ljcohen, @charlesreid1

v1.0

Fix a typo.

v1.0rc2

Update README.rst

RC1: Some BUSCO fixes for bioconda

v1.0.rc1

Bump version

dammit 1.0 release candidate 0

This release represents a significant refactor of dammit. It supports updated versions of TransDecoder and BUSCO (3.0.2); all v2 BUSCO databases; removes crb-blast, ruby, and NCBI BLAST dependencies; fixes a lot of bugs; and is generally more stable and easy to use and install.

1.0 Backport

This is a final release of v0.3.2 before 1.0 is pushed out. It brings in a number of bugfixes from 1.0:

• Fixes the empty transcript names caused from TransDecoder 3.0 incompat
• Fixes the float NaN error with Pandas 1.19.1 #78
• Fixes infernal coord issues #70
• Allows BUSCO to use v1.22
• Updates v1 BUSCO database URLs
• Fixes gnu-parallel command that was broken on OSX
• Allows use of --sshloginfile for clusters

To install, do:
pip install dammit==0.3.2

Moar Parallel, Less Bugs

Changes:

• Fixes the broken parallel hmmscan command. Sorry bout that!
• Adds parallel support to cmscan.
• Adds a bunch more tests.
• Reorganizes the test suite.
• Remove the deprecated CRBB module and its scikit-learn dependency (development on that is now over in https://github.com/camillescott/shmlast)
• Slight modifications to the install instructions.

Update in the usual way with:

pip install -U --no-deps dammit

Unless otherwise unable, it's also good to update pandas:

conda update pandas numexpr

Parallelize all the things

This release updates the lastal and hmmscan tasks to use GNU parallel for multiprocessing. This means that both should be much faster, and lastal will no longer fail when the -P option is unavailable. Fixes #53 and #19.

pip install -U --no-deps dammit