Prediction module #14
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Minor refactoring Adds Augustus to conda environment definition file
We have models now according to the training specification, only missing some tests and printing as either a list that can be used by gff2gb to extract or gff HashableTranscript provides hash and simpler repr for Mikado.Transcripts
Collate augustus output predictions Add CLI arguments for: - Re-training if the species is already present - Intron hints - Optionally optimising augustus and number of folds parameter for optimisation - Make certain CLI inputs required Selective training based on input config_path Adding intron hints parameter and force training parameter (for existing species) Preparing for many runs (gold+silver, homology preference, etc) Safer bash with set -euxo pipefail
# Conflicts: # annotation/__init__.py
Fix augustus training condition for existing species Ensure sampling is reproducible and generates the right ratio of mono/multi exonic models
Make scripts executable Carry the index of the fasta reference alongside it
Always turn on UTR training on augustus
Use a file of sources and priorities for each evidence type for each augustus run, this allows running as many augustus instances as parameter files ther are in the CLI input.
Quiet down wget download
- Add a standalone python3 compatible bam2wig script based on rseqc's bam2wig, this new script also accepts csi indices - Improve checks on generate_augustus_hint_parameters script - Generate a single 'base' expressed exon hints file that is then customised per augustus run - Collate repeats, expression, and intron hints into the WDL - Add EVM to reat.yml
- EVM process for combining predictions - Input of weights for EVM - Minor updates to augustus.wdl (bugfix) - Add another CQ run which predicts all models (including for locus where a model was provided)
Basic functionality completed, now need to add chunking for Augustus
Rename AugustusTest to AugustusAbinitio
# Conflicts: # annotation/__init__.py
- HQ/LQ assembly and protein_alignments can be used as evidence or for defining alternative splicing or UTRs in mikado (if present) - Add parameters for controlling gene predictor runs - Automatically determine if running Augustus with or without hints from the parameters - Preprocess repeat gff for use as Augustus hints
Remove unused __init__.py in script
Pass length check on both transcriptome and homology models Fix protein_alignments inputs to EVM Keep raw output from the gene predictors Fix zff_to_gff script
Ensure ChangeSource produces regular output Fix parameter parsing for 0 - 100 int ranges
* gff_to_evm script to create EVM spec GFF files
Remove exception when using | head after gff_to_evm
Combines ArgumentDefaultsHelpFormatter & RawDescriptionHelpFormatter in a single class
# Conflicts: # annotation/__main__.py
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