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Rneat demo
Joshua Allen edited this page Sep 26, 2025
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1 revision
Welcome to the rusty-neat wiki!
(my_python) joshfactorial@uber-jason:~/code$ ./rusty-neat/target/release/rneat --help Usage: rneat [OPTIONS] [SUB-COMMAND]
SUB-COMMANDS:
gen-reads Generates reads for an input dataset
filter-reads Filters the output of gen-reads
help Print this message or the help of the given subcommand(s)
Options:
--log-level [<log_level>] Sets the log level for the display log. [default: trace] [possible values: trace, debug, info, warn, error, off]
--log-dest <log_dest> Sets the log destination (full path with full filename) for the written log
-h, --help Print help
(my_python) joshfactorial@uber-jason:~/code$ ./rusty-neat/target/release/rneat gen-reads --help
Generates reads for an input dataset
Usage: rneat gen-reads --configuration-yaml <configuration_yaml>
Options:
-c, --configuration-yaml <configuration_yaml> Path to configuration file.
-h, --help Print help
Filters the output of gen-reads
Usage: rneat filter-reads --configuration-yaml <configuration_yaml>
Options:
-c, --configuration-yaml <configuration_yaml> Path to configuration file.
-h, --help Print help
# Full path to reference in fasta format
reference: .
# Whole number length of reads
read_len: .
# Whole number target coverage value
coverage: .
# float giving the average mutation rate
mutation_rate: .
# integer value for ploidy
ploidy: .
# boolean
paired_ended: .
# floats that give the mean and standard deviation of the fragments desired
fragment_mean: .
fragment_st_dev: .
# Boolean values
produce_vcf: .
produce_fastq: .
# true or false (default false, to avoid destroying data)
overwrite_output: .
# the directory where you want to write files
output_dir: .
# the common name given to all output files (e.g., "TEST" => TEST_r1.fastq, TEST.vcf, TEST.bam)
output_filename: .
# input files (full paths to files)
# Note that these are not yet active
# mutation_model: .
# fragment_model: .
# sequence_error_model: .
# inclusion_bed: .
Input is a list of files to filter, which can be 1 file or many files, so long as they are either fastq or vcf and were generated by rneat (see README caveats about contig names). The keyword is appended to all filenames.
# You must input a bed file with valid regions
# for the fastq and/or vcf files to be filtered
bed_file: # required
# You must input a list of files to filter.
# The list can be one file.
files_to_filter: [
# required, in list form
]
# This is the filter key that will be appended to the end of the filename
# before the extensions. The default is "_filtered" i.e.,
# "output_file.vcf.gz" becomes "output_file_filtered.vcf.gz"
filter_key: .
(my_python) joshfactorial@uber-jason:~/code$ ./rusty-neat/target/release/rneat gen-reads -c simple_template.yml
log dest = "/home/joshfactorial/code/.neat.log"
05:44:13 [INFO] ////////////// Welcome to rneat! \\\\\\\\\\\\\\
05:44:13 [INFO] Running gen-reads to generate read data.
05:44:13 [INFO] ////////////// Welcome to rusty-neat read generator! \\\\\\\\\\\\\\\
05:44:14 [INFO] Using Configuration file input: "simple_template.yml"
05:44:14 [INFO] Running rusty-neat to generate reads on "/home/joshfactorial/code/ecoli.fa" with...
05:44:14 [INFO] Running rusty-neat to generate reads on /home/joshfactorial/code/ecoli.fa with...
05:44:14 [INFO] >read length: 151
05:44:14 [INFO] >coverage: 10
05:44:14 [INFO] >mutation rate: 0.001
05:44:14 [INFO] >ploidy: 2
05:44:14 [INFO] >paired ended: false
05:44:14 [INFO] Producing fastq file:
05:44:14 [INFO] > "/home/joshfactorial/code/neat_out_r1.fastq.gz"
05:44:14 [INFO] Seed string to regenerate these exact results: 2025 09 26 05 44 14 114763279
05:44:14 [INFO] ////////////// Configuration successuful! Ready to run! \\\\\\\\\\\\\
05:44:14 [INFO] Created temp dir at TempDir { path: "/tmp/.tmp8CnACf" }
05:44:14 [INFO] Generate quality score model
05:44:14 [INFO] Generate mutation model
05:44:14 [INFO] Generate fragment length model
05:44:14 [INFO] Generate sequencing error model
05:44:14 [INFO] Generate quality score model
05:44:14 [INFO] Reading fasta file: /home/joshfactorial/code/ecoli.fa
05:44:14 [INFO] Generating simulated dataset
05:44:15 [INFO] Producing final fastq(s) file(s)
05:44:15 [INFO] Successfully wrote fastq file: "/home/joshfactorial/code/neat_out_r1.fastq.gz"
05:44:15 [INFO] Successfully produced unfiltered output file: ["/home/joshfactorial/code/neat_out_r1.fastq.gz"]
05:44:15 [INFO] rneat gen-reads completed successfully
05:44:15 [INFO] Processing finished in 2575 milliseconds
05:44:15 [INFO] Processing finished in 2 seconds