"I love writing BLAST parsers!" -- no one, ever
dammit is a simple de novo transcriptome annotator. It was born out of the observation that: annotation is mundane and annoying; all the individual pieces of the process exist already; and, the existing solutions are overly complicated or rely on crappy non-free software.
Science shouldn't suck for the sake of sucking, so dammit attempts to make this sucky part of the process suck a little less.
Basic Usage
Install dammit with bioconda.
conda create -n dammit-env python=3 dammit
conda activate dammit-env
Download and install a subset of the databases:
dammit databases --install --quick
And the annotate with:
dammit annotate <transcriptome_fasta>
Head over to the docs for much more detailed information!
Acknowledgements
I've received input and advice from a many sources, including but probably not limited to: C Titus Brown, Matt MacManes, Chris Hamm, Michael Crusoe, Russell Neches, Luiz Irber, Lisa Cohen, Tessa Pierce, Sherine Awad, and Tamer Mansour.
CS was funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513 through May 2016, and now receives support from the Gordon and Betty Moore Foundation under Award number GBMF4551.