• pyclustering
• pysam
• pomegranate

Execute the train.py script:

python3 train.py

The train.py reads the local config.json file that provides configuration parameters for the training. Below is an explanation of the entries in config.json

• regions: is a map with start and end lists of the regions to be used. Regions do not have to be consecutive

 "regions":{
      "start":[1000000],
      "end":[10000000]
  },

• "chromosome": is single valued and specifies which chromosome to use

"chromosome": "chr1",

• reference_file: specifies the refernce sequence file
• no_wga_file: specifies the non-WGA-treated sequence file
• test_file: specifies the WGA-treated sequence file
• debug: a map with debug options currently only log_bam_for_debug flag is supported. If set to true the bam entries read for the regions are written in the logger_file .
• "window_size": The window size to use
• "fill_missing_window_data": flag indcating if missing window RD counts should be filled
• "fill_missing_window_data_factor": The factor to use for filling missing window data
• "quality_threshold": Threshold to read a sequence from bam. If ```null`` no threshold is used,
• "save_windows": Flag indicating if the created windows should be saved,
• "windows_filename":The fille to save the windows,
• "remove_windows_with_N": Flag indicating that any window containing an N should be removed,
• "mark_N_windows": Flag indicating whethre to mark windows containig an N,
• "mark_for_N_windows": The mark to use for the N windows
• "outlier_remove": Map indicating how to mark outlier windows

 "outlier_remove":{

    "name":"zscore",
    "config":{
      "sigma_factor":5,
      "use_both_ends":false
    },
  },

  "outlier_remove":{
   "name": "means_cutoff",
    "config":{
      "mu_limits":{"wga_mu": 140.0, "no_wga_mu": 120.0},
    }
 }

• "clusterer": A map with the properties of the clustering method to be used

 "clusterer":{
    "name":"kmedoids",
    "config":{
    "init_cluster_idx":"random_from_data", or a list of indices
    "metric":"MANHATAN", 
    "metric_degree": 4, # only used when MINKOWSKI metric is applied
    "features":["mean"],
    "n_clusters":4
    }
  },

Valid metrics are:

• "MANHATAN"

• "EUCLIDEAN"

• "CHEBYSHEV"

• "MINKOWSKI"

• "label_clusters": Flag indicating if the clusters should be labelled

• "labeler": If label_clusters is set to true this map contains the properties of the labeler

"label_clusters": true,
  "labeler":{
    "name":"mean_diff",
    "tuf_mean_min": 1.5,
    "tuf_mean_max": 8.5,
    "states":["DELETE", "OTHER", "OTHER", "TUF"]
  },

• "cluster_distribution": Map indicating how the densities of each formed cluster should be modelled

"cluster_distribution":{
    "name": "gmm",
    "config":{
      "distributions":{
          "TUF":{
              "type":"gmm",
              "dists":["normal", "uniform"],
              "weights":null,
              "uniform_params":[2.0, 8.0] # U(2.0, 8.0)
          },
          "OTHER":{
              "type":"distribution", # use gmm for multinomial
              "dists":["normal"]
          },
          "DELETE":{
              "type":"distribution",
              "dists":["normal"]
          }
      }
    }
  },

• "HMM": Properties for HMM model

"HMM": {
    "name":"HMM_Model", # name of the model
    "train":false, # whether train or not
    "train_solver": "baum-welch", # if train how: "baum-welch" or "viterbi"
    "lr_decay":0.7,
    "inertia":null,
    "verbose":true,
    "save_model":true,
    "save_hmm_filename":"HMM_Model",
    "start_prob":{
      "OTHER_0": 0.475, # not used
      "OTHER_1": 0.475, # not used
      "DELETE": 0.0166,
      "TUF": 0.0166
    },
    "train_sequence_size": 100,
    "train_sequence_source": "region",
    "train_n_sequences_per_source":10000,
    "train_windowtype":"both"
  },

• "logger_file": The filename for the logs,
• "logger_level": Minimum level of logging