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Agecrack-ng is a tool for searching and extracting age-related features from data.

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Agecrack-ng

Agecrack-ng is a tool for searching and extracting age-related features from data.

Run

# prepare environment
brew install mmseqs2

# clone
git clone git@github.com:moozeq/agecrack-ng.git
cd agecrack-ng

# setup venv
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

# run
./agecrack-ng.py -h
usage: agecrack-ng.py [-h] [--mode {predictor,ontology,ontology-parse,vectors,prepare,mmseqs-estimation}] [--model {rf,encv,en}] [--filters FILTERS [FILTERS ...]]
                      [--filter-class FILTER_CLASS] [--exclude EXCLUDE [EXCLUDE ...]] [--extract-threshold EXTRACT_THRESHOLD] [--anage ANAGE] [--ncbi NCBI] [--skip]
                      [--count-proteins] [--ontology-plots-freqs] [--reload] [--models-reuse] [--models-params MODELS_PARAMS] [--models-rand MODELS_RAND]
                      [--models-stratify] [--models-bins MODELS_BINS] [--models-plots-show] [--models-plots-unprocess] [--models-plots-annotate]
                      [--models-plots-annotate-threshold MODELS_PLOTS_ANNOTATE_THRESHOLD] [--models-plots-clusters-count MODELS_PLOTS_CLUSTERS_COUNT]
                      [--mmseq-params MMSEQ_PARAMS] [--mmseq-threshold MMSEQ_THRESHOLD] [--mmseq-vectors-mode {count,bool}] [--mmseq-force] [--plot-anage-hists] [-v]

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Tool for searching and extracting age-related features from data.

optional arguments:
  -h, --help            show this help message and exit
  --mode {predictor,ontology,ontology-parse,vectors,prepare,mmseqs-estimation}
                        Select mode for running the program:
                             - "predictor" gives single best predictor for longevity based on predefined parameters
                             - "ontology" runs analysis for clusters ontology and correlation with longevity
                             - "ontology-parse" parses files obtained in ontology analysis
                             - "vectors" produces additional visualization of species genes vectors
                             - "prepare" download all data, cluster them and prepare for further analysis
                             - "mmseqs-estimation" produces additional plots for mmseqs params estimation
                         (default: predictor)
  --model {rf,encv,en}  ML model (default: rf)
  --filters FILTERS [FILTERS ...]
                        Filters used for extracting proteins sequences, examples in "filters.json" file, when list with empty string is provided (`['']`) - no filtering is applied (default: [''])
  --filter-class FILTER_CLASS
                        Filter species from specific phylo class (e.g. "Mammalia") (default: None)
  --exclude EXCLUDE [EXCLUDE ...]
                        List of excluded species from analysis (default: [])
  --extract-threshold EXTRACT_THRESHOLD
                        Filter out species with count of genes below threshold (default: 1)
  --anage ANAGE         AnAge database file (default: data/anage_data.txt)
  --ncbi NCBI           NCBI eukaryotes database file (default: data/eukaryotes.txt)
  --skip                Skip downloading and extracting part, use it to speed up when trying different models, (option is omitted when running mmseq) (default: False)
  --count-proteins      Count proteins for proper log messages (can impact performance greatly) (default: False)
  --ontology-plots-freqs
                        Show and save plot for clusters frequencies at first 10 places instead importance (default: False)
  --reload              Reload produced files, set when changing thresholds (default: False)
  --models-reuse        Reuse ML models from files if exist (default: False)
  --models-params MODELS_PARAMS
                        Specify params for model as json dict, if not specified the ones from "grid_params.json" will be used (default: None)
  --models-rand MODELS_RAND
                        Random state for splitting data for training and testing (default: 17)
  --models-stratify     Try to stratify dataset using bins (default: False)
  --models-bins MODELS_BINS
                        How many bins for stratifying data, if not specified - number of species divided by 2 (default: 0)
  --models-plots-show   Show plots for each model (default: False)
  --models-plots-unprocess
                        Unprocess data for models predicted plots (default: False)
  --models-plots-annotate
                        Annotate points on models plots with species names (default: False)
  --models-plots-annotate-threshold MODELS_PLOTS_ANNOTATE_THRESHOLD
                        Difference between predicted and known lifespan that should be annotated (default: 0.5)
  --models-plots-clusters-count MODELS_PLOTS_CLUSTERS_COUNT
                        Up to how many most important clusters should be shown on an ontology plot (default: 30)
  --mmseq-params MMSEQ_PARAMS
                        Specify params for mmseqs as json dict, params = "min_seq_id", "c", "cov_mode" (default: {"min_seq_id": 0.8, "c": 0.8, "cov_mode": 0})
  --mmseq-threshold MMSEQ_THRESHOLD
                        Clusters under strength of this threshold will be filter out (default: 0)
  --mmseq-vectors-mode {count,bool}
                        Vectors mode for species, use "bool" to obtain boolean vectors instead of integer vectors with sequences counts (default: count)
  --mmseq-force         Force re-running mmseq (default: False)
  --plot-anage-hists    Plot AnAge database histograms (default: False)
  -v, --verbose         Increase verbosity (default: 0)

Analysis

Vertebrates

# best vertebrates predictor
./agecrack-ng.py -vv --mode predictor --model rf --filters repair --mmseq-vectors-mode bool --models-rand 1 --mmseq-params '{"min_seq_id": 0.8, "c": 0.2, "cov_mode": 2}' --models-params '{"n_estimators": 300, "max_depth": 18}'

# plots on unprocessed data
./agecrack-ng.py -vv --mode predictor --model rf --filters repair --mmseq-vectors-mode bool --models-rand 1 --mmseq-params '{"min_seq_id": 0.8, "c": 0.2, "cov_mode": 2}' --models-params '{"n_estimators": 300, "max_depth": 18}' --models-plots-unprocess

# gather multiple models and analyse them all
./agecrack-ng.py -vv --mode ontology --model rf --filters repair --mmseq-vectors-mode bool --models-rand 1 --mmseq-params '{"min_seq_id": 0.8, "c": 0.2, "cov_mode": 2}'

train-vertebrates test-vertebrates

Mammalia

# best mammalia predictor
./agecrack-ng.py -vv --mode predictor --model rf --filter-class Mammalia --exclude 'Homo sapiens' --extract-threshold 1000 --models-plots-annotate --models-rand 17 --mmseq-params '{"min_seq_id": 0.8, "c": 0.8, "cov_mode": 0}' --models-params '{"n_estimators": 30, "max_depth": 7}'

# plots on unprocessed data
./agecrack-ng.py -vv --mode predictor --model rf --filter-class Mammalia --exclude 'Homo sapiens' --extract-threshold 1000 --models-plots-annotate --models-plots-annotate --models-plots-annotate-threshold 15 --models-rand 17 --mmseq-params '{"min_seq_id": 0.8, "c": 0.8, "cov_mode": 0}' --models-params '{"n_estimators": 30, "max_depth": 7}'

# gather multiple models and analyse them all
./agecrack-ng.py -vv --mode ontology --model rf --filter-class Mammalia --exclude 'Homo sapiens' --extract-threshold 1000 --models-plots-annotate --models-rand 17 --mmseq-params '{"min_seq_id": 0.8, "c": 0.8, "cov_mode": 0}'

train-mammalia test-mammalia

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Agecrack-ng is a tool for searching and extracting age-related features from data.

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