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Support Scripts

1. dataset_partitioner.sh

Partition given blow5 in to train and test splits with given number of reads for each

  • Args
    • $1 - path to source BLOW5
    • $2 - Required minimum read length for train/test sets
    • $3 - Number of reads for train set
    • $4 - Number of reads for test set
    • $5 - Output file/dataset name
sh dataset_partitioner.sh covid.blow5 4500 20000 20000 covid

2. baseline.sh

Run the baseline analysis for given dataset

  • Args
    • $1 - Path to positive blow5 file
    • $2 - Path to negative blow5 file
    • $3 - Path to positive fastq file
    • $4 - Path to negative fastq file
    • $5 - Path to positive reference gemome
    • $6 - Path to negative reference gemome
    • $7 - Required base length
sh baseline.sh covid.blow5 zymo.blow5 covid.fastq zymo.fastq covid.ref.fasta zymo-ref.fasta 300

3. trim-slow5-reads.sh

Provide trimmed Slow5 reads with given raw signal length

  • Args
    • $1 - Slow5 file
    • $2 - Expected raw signal length to have after trimming
sh trim-slow5-reads.sh covid.slow5 4500

4. guppy_fast_minimap2.sh

Evaluator for Guppy_fast+Minimap2 read classification accuracy

  • Args
    • $1 - Path to targeted species test data fastq
    • $2 - Path to non-targeted species test data fastq
    • $3 - Path to targeted species reference genome
    • $4 - Path to non-targeted species reference genome
python guppy_fast_minimap2.sh test-covid.fastq test-zymo.fastq covid-ref.fasta zymo-ref.fasta

5. mycopy.py

Custom copy script with enhanced uses to copy/move/delete/rename

  • Args
    • s - The path to source of files
    • d - The path to destination to be copied
    • i - Iterate through files including child directories (default=True)
    • ext - File extension type to be copied (default='' -> any)
    • c - Amount of files to be copied/moved/deleted (default=0 -> means all files)
    • cut - Is cut and paste files (default=False)
    • del - Is delete source files (default=False)
    • rn - Suffix to rename files while copying files (default='')
python mycopy.py -s <src_dir> -d <dest_dir> -ext fast5 -c 10000 -cut True -rn _zymo

6. npy_plotter.py

Plot the numpy dump files

  • Args
    • np - The path to npy files directory
    • mad - Median absolute deviation value for data normalization (default=3)
    • rep - Is repeatedly normalized or not (default=False)
python npy_plotter.py -np <npy_dir> -mad 5

7. npy_reader.py

Print data array in numpy dump

  • Args
    • np - The path to npy file
python npy_reader.py -np <npy_file>