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Command-Line Help for deepbiop-cli

This document contains the help content for the deepbiop-cli command-line program.

Command Overview:

deepbiop-cli

CLI tool for Processing Biological Data.

Usage: deepbiop-cli [OPTIONS] [COMMAND]

Subcommands:
  • count-chimeric — Count chimeric reads in a BAM file
  • bam-to-fq — BAM to fastq conversion
  • fq-to-fa — Fastq to fasta conversion
  • fa-to-fq — Fasta to fastq conversion
  • fa-to-parquet — Fasta to parquet conversion
  • fq-to-parquet — Fastq to parquet conversion
  • extract-fq — Extract fastq reads from a fastq file
  • extract-fa — Extract fasta reads from a fasta file
  • fqs-to-one — Multiple Fastqs to one Fastq conversion
  • fas-to-one — Multiple Fastas to one Fasta conversion
Options:
  • --generate <GENERATOR>

Possible values: bash, elvish, fish, powershell, zsh

  • -v, --verbose — Increase logging verbosity
  • -q, --quiet — Decrease logging verbosity

deepbiop-cli count-chimeric

Count chimeric reads in a BAM file

Usage: deepbiop-cli count-chimeric [OPTIONS] [bam]...

Arguments:
  • <bam> — path to the bam file
Options:
  • -t, --threads <THREADS> — threads number

Default value: 2

deepbiop-cli bam-to-fq

BAM to fastq conversion

Usage: deepbiop-cli bam-to-fq [OPTIONS] [bam]...

Arguments:
  • <bam> — path to the bam file
Options:
  • -t, --threads <THREADS> — threads number

Default value: 2 * -c, --compressed — output bgzip compressed fastq file

deepbiop-cli fq-to-fa

Fastq to fasta conversion

Usage: deepbiop-cli fq-to-fa [OPTIONS] [fq]...

Arguments:
  • <fq> — path to the fq file
Options:
  • -t, --threads <THREADS> — threads number

Default value: 2

deepbiop-cli fa-to-fq

Fasta to fastq conversion

Usage: deepbiop-cli fa-to-fq [OPTIONS] [fa]...

Arguments:
  • <fa> — path to the fa file
Options:
  • -t, --threads <THREADS> — threads number

Default value: 2

deepbiop-cli fa-to-parquet

Fasta to parquet conversion

Usage: deepbiop-cli fa-to-parquet [OPTIONS] <fa>

Arguments:
  • <fa> — path to the fa file
Options:
  • --chunk — if convert the fa file to parquet by chunk or not
  • --chunk-size <CHUNK_SIZE> — chunk size

Default value: 1000000 * --output <result> — result path * -t, --threads <THREADS> — threads number

Default value: 2

deepbiop-cli fq-to-parquet

Fastq to parquet conversion

Usage: deepbiop-cli fq-to-parquet [OPTIONS] <fq>

Arguments:
  • <fq> — path to the fq file
Options:
  • --chunk — if convert the fq file to parquet by chunk or not
  • --chunk-size <CHUNK_SIZE> — chunk size

Default value: 1000000 * --output <output> — result path * -t, --threads <THREADS> — threads number

Default value: 2

deepbiop-cli extract-fq

Extract fastq reads from a fastq file

Usage: deepbiop-cli extract-fq [OPTIONS] <fq>

Arguments:
  • <fq> — path to the fq file
Options:
  • --reads <reads> — Path to the selected reads
  • --number <number> — The number of selected reads by random
  • --output <output> — output bgzip compressed file
  • -t, --threads <THREADS> — threads number

Default value: 2 * -c, --compressed — output bgzip compressed fastq file

deepbiop-cli extract-fa

Extract fasta reads from a fasta file

Usage: deepbiop-cli extract-fa [OPTIONS] <fa>

Arguments:
  • <fa> — path to the bam file
Options:
  • --reads <reads> — Path to the selected reads
  • --number <number> — The number of selected reads by random
  • --output <output> — output bgzip compressed file
  • -t, --threads <THREADS> — threads number

Default value: 2 * -c, --compressed — output bgzip compressed fasta file

deepbiop-cli fqs-to-one

Multiple Fastqs to one Fastq conversion

Usage: deepbiop-cli fqs-to-one [OPTIONS] --output <output> [fqs]...

Arguments:
  • <fqs> — path to the fq file
Options:
  • --output <output> — output bgzip compressed file
  • -t, --threads <THREADS>

Default value: 2

deepbiop-cli fas-to-one

Multiple Fastas to one Fasta conversion

Usage: deepbiop-cli fas-to-one [OPTIONS] --output <output> [fas]...

Arguments:
  • <fas> — path to the fa file
Options:
  • --output <output> — output bgzip compressed file
  • -t, --threads <THREADS>

Default value: 2

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