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Model Testing

Once we trained the model on some WT and IVT reads we tested our model's accuracy on 500 hold out WT and IVT reads.

  • In order to run training you need to alter the paths in the config file inference.config.json

    • Under samples there is one named "wild_type". You need to change the paths to the corresponding file within your path system 
      "positions_file": "/home/ubuntu/yeast_rrna_modification_detection/training/small_5mer/yeast_18S_25S_modified.positions",
"fast5_dirs": ["/home/ubuntu/"],
"bwa_reference": "/home/ubuntu/yeast_rrna_modification_detection/data_preprocessing/reference/yeast_25S_18S.fa",
"readdb": "/home/ubuntu/fastq/20210410_R941_WT_YPD/20210410_1830_MN20528_AGN282_f7dbe316/20210410_1830_MN20528_AGN282_f7dbe316.inference.readdb",
"alignment_file": "/home/ubuntu/fastq/20210410_R941_WT_YPD/20210410_1830_MN20528_AGN282_f7dbe316/20210410_1830_MN20528_AGN282_f7dbe316.2308.sorted.bam",
    • Under samples there is one named "ivt". You need to change the paths to the corresponding file within your path system 
      "positions_file": "/home/ubuntu/yeast_rrna_modification_detection/training/small_5mer/yeast_18S_25S_canonical.positions",
"fast5_dirs": ["/home/ubuntu/"],
"bwa_reference": "/home/ubuntu/yeast_rrna_modification_detection/data_preprocessing/reference/yeast_25S_18S.fa",
"readdb": "/home/ubuntu/fastq/20191014_R941_IVT/20191014_1845_MN20528_FAL23261_9a8cb226/20191014_1845_MN20528_FAL23261_9a8cb226.inference.readdb",
"alignment_file": "/home/ubuntu/fastq/20191014_R941_IVT/20191014_1845_MN20528_FAL23261_9a8cb226/20191014_1845_MN20528_FAL23261_9a8cb226.2308.sorted.bam",
    • Finally, you need to put the path to signalAlign's bin, the base model, output dir, job count (n threads), and the ambig model. 
      "path_to_bin": "/home/ubuntu/src/signalAlign/bin",
"template_hmm_model": "/home/ubuntu/yeast_rrna_modification_detection/testing/yeast_rrna_ivt_wt_trained_071521.model",
"output_dir": "/home/ubuntu/training/ivt_vs_wt",
"ambig_model": "/home/ubuntu/yeast_rrna_modification_detection/training/small_5mer/small_variants.model",
"job_count": 8

  • runSignalAlign.py run --config /home/ubuntu/yeast_rrna_modification_detection/testing/inference.config.json

  • embed_main sa2bed -d /home/ubuntu/testing/tempFiles_alignment/ivt/ -a /home/ubuntu/yeast_rrna_modification_detection/training/small_5mer/small_variants.model -o /home/ubuntu/testing/tempFiles_alignment/ivt.bed -t 96 -c B --overwrite --rna

  • embed_main sa2bed -d /home/ubuntu/testing/tempFiles_alignment/wild_type/ -a /home/ubuntu/yeast_rrna_modification_detection/training/small_5mer/small_variants.model -o /home/ubuntu/testing/tempFiles_alignment/wild_type.bed -t 96 -c B --overwrite --rna

  • plot_multiple_variant_accuracy.py --config /home/ubuntu/yeast_rrna_modification_detection/testing/testing_accuracy.config.json