Running dnaapler

For all subcommands, dnaapler requires an input FASTA file using the -i or --input parameters.

It is also highly recommended to specify an output directory using the -o or --output parameters, otherwise dnaapler will write the output to a directory named output.dnaapler by default.

You can modify the prefix for the output files from dnaapler to whatever you please with the -p or --prefix parameters.

You can use BLAST with multiple threads using the -t or --threads parameters and modify the BLAST evalue with the -e or --evalue parameter.

dnaapler will not overwrite an output directory if it already exists by default. To force overwrite, please use -f or --force.

Finally, for the BLAST based subcommands (chromosome, phage, plasmid, custom or all), if no BLAST hit is found, by default dnaapler will error and exit.

However, you can decide to autocomplete dnaapler using the -a or --autocomplete parameters along with mystery or nearest, which will then run those subcommands to reorient your sequence.

Also, a seed value using --seed_value can be specified with dnaapler to ensure that dnaapler mystery (or when austocomplete is used with -a mystery) to ensure dnaapler is reproducible in workflows.

all

dnaapler all is designed to simultaneously orient multiple contigs that can be a mix of chromosomes, plasmids and phages. It will also work on just 1 contig.

If a contig has BLAST hits for both dnaA and terL or repA, dnaA will be chosen for reorientation.

If a contig has BLAST hits for both terL and repA (but not dnaA), repA will be chosen for reorientation.

You can also specify a text file with --ignore that lists all contigs (based on their header) to be ignored during reorientation.

e.g. the file (ignored_contigs.txt) needs to be formatted as follows:

contig_1
contig_2

Example usage to reorient a number of contigs in input.fasta, ignoring all contigs with headers denoted in ignored_contigs.txt

dnaapler all -i input.fasta -o output_directory_path -t 8  --ignore ignored_contigs.txt

Usage: dnaapler all [OPTIONS]

  Reorients contigs to begin with any of dnaA, repA or terL

Options:
  -h, --help               Show this message and exit.
  -V, --version            Show the version and exit.
  -i, --input PATH         Path to input file in FASTA format  [required]
  -o, --output PATH        Output directory   [default: output.dnaapler]
  -t, --threads INTEGER    Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
  -f, --force              Force overwrites the output directory
  -e, --evalue TEXT        e value for blastx  [default: 1e-10]
  --ignore PATH            Text file listing contigs (one per row) that are to
                           be ignored
  -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if
                           BLAST based approach fails. Must be one of: none,
                           mystery, largest, or nearest [default: none]
  --seed_value INTEGER     Rand

chromosome

Example usage with mystery as the autocomplete command and a random seed of 245 for reproducibility and with 8 threads for BLAST:

dnaapler chromosome -i input.fasta -o output_directory_path -p my_bacteria_name -t 8 -a mystery --seed_value 245

Usage: dnaapler chromosome [OPTIONS]

  Reorients your genome to begin with the dnaA chromosomal replication
  initiation gene

Options:
  -h, --help               Show this message and exit.
  -V, --version            Show the version and exit.
  -i, --input PATH         Path to input file in FASTA format  [required]
  -o, --output PATH        Output directory   [default: output.dnaapler]
  -t, --threads INTEGER    Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
  -f, --force              Force overwrites the output directory
  -e, --evalue TEXT        e value for blastx  [default: 1e-10]
  -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if
                           BLAST based approach fails. Must be one of: none,
                           mystery or nearest [default: none]
  --seed_value INTEGER     Random seed to ensure reproducibility.  [default:
                           13]

phage

Example usage with no autocomplete command:

dnaapler phage -i input.fasta -o output_directory_path -p my_phage_name -t 8 

Usage: dnaapler phage [OPTIONS]

  Reorients your genome to begin with the terL large terminase subunit

Options:
  -h, --help               Show this message and exit.
  -V, --version            Show the version and exit.
  -i, --input PATH         Path to input file in FASTA format  [required]
  -o, --output PATH        Output directory   [default: output.dnaapler]
  -t, --threads INTEGER    Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
  -f, --force              Force overwrites the output directory
  -e, --evalue TEXT        e value for blastx  [default: 1e-10]
  -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if
                           BLAST based approach fails. Must be one of: none,
                           mystery or nearest [default: none]
  --seed_value INTEGER     Random seed to ensure reproducibility.  [default:
                           13]

plasmid

Example usage with no autocomplete command:

dnaapler plasmid -i input.fasta -o output_directory_path -p my_plasmid_name -t 8 

Usage: dnaapler plasmid [OPTIONS]

  Reorients your genome to begin with the repA replication initiation gene

Options:
  -h, --help               Show this message and exit.
  -V, --version            Show the version and exit.
  -i, --input PATH         Path to input file in FASTA format  [required]
  -o, --output PATH        Output directory   [default: output.dnaapler]
  -t, --threads INTEGER    Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
  -f, --force              Force overwrites the output directory
  -e, --evalue TEXT        e value for blastx  [default: 1e-10]
  -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if
                           BLAST based approach fails. be one of: none,
                           mystery or nearest [default: none]
  --seed_value INTEGER     Random seed to ensure reproducibility.  [default:
                           13]

custom

To run dnaapler custom, you need to prefix an Amino Acid FASTA file containing the desired custom database gene using -c or --custom_db.

Example usage:

dnaapler custom -i input.fasta -o output_directory_path -p my_plasmid_name -t 8 -c custom_db.faa

Usage: dnaapler custom [OPTIONS]

  Reorients your genome with a custom database

Options:
  -h, --help               Show this message and exit.
  -V, --version            Show the version and exit.
  -i, --input PATH         Path to input file in FASTA format  [required]
  -o, --output PATH        Output directory   [default: output.dnaapler]
  -t, --threads INTEGER    Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
  -f, --force              Force overwrites the output directory
  -e, --evalue TEXT        e value for blastx  [default: 1e-10]
  -c, --custom_db PATH     FASTA file with amino acids that will be used as a
                           custom blast database to reorient your sequence
                           however you want.  [required]
  -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if
                           BLAST based approach fails. Must be one of: none,
                           mystery or nearest [default: none]
  --seed_value INTEGER     Random seed to ensure reproducibility.  [default:
                           13]

mystery

dnaapler mystery will reorient your genome to begin with a random coding sequence (CDS) (as predicted by Pyrodigal).

Example usage:

dnaapler mystery -i input.fasta -o output_directory_path -t 8 

Usage: dnaapler mystery [OPTIONS]

  Reorients your genome with a random CDS

Options:
  -h, --help             Show this message and exit.
  -V, --version          Show the version and exit.
  -i, --input PATH       Path to input file in FASTA format  [required]
  -o, --output PATH      Output directory   [default: output.dnaapler]
  -t, --threads INTEGER  Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT      Prefix for output files  [default: dnaapler]
  -f, --force            Force overwrites the output directory
  --seed_value INTEGER   Random seed to ensure reproducibility.  [default: 13]

nearest

dnaapler nearest will reorient your genome to begin the first coding sequence (CDS) as predicted by Pyrodigal.

Example usage:

dnaapler nearest -i input.fasta -o output_directory_path -t 8 

Usage: dnaapler nearest [OPTIONS]

  Reorients your genome the begin with the first CDS as called by pyrodigal

Options:
  -h, --help             Show this message and exit.
  -V, --version          Show the version and exit.
  -i, --input PATH       Path to input file in FASTA format  [required]
  -o, --output PATH      Output directory   [default: output.dnaapler]
  -t, --threads INTEGER  Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT      Prefix for output files  [default: dnaapler]
  -f, --force            Force overwrites the output directory

largest

dnaapler largest will reorient your genome to begin the largest coding sequence (CDS) as predicted by Pyrodigal.

Example usage:

dnaapler largest -i input.fasta -o output_directory_path -t 8 

Usage: dnaapler nearest [OPTIONS]

  Reorients your genome the begin with the largest CDS as called by pyrodigal

Options:
  -h, --help             Show this message and exit.
  -V, --version          Show the version and exit.
  -i, --input PATH       Path to input file in FASTA format  [required]
  -o, --output PATH      Output directory   [default: output.dnaapler]
  -t, --threads INTEGER  Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT      Prefix for output files  [default: dnaapler]
  -f, --force            Force overwrites the output directory

bulk

dnaapler bulk is designed to simultaneously orient multiple genomes. You must also specify -m or --mode with either chromosome, phage, plasmid or custom to tell dnaapler what mode to run. It will default to -m chromosome. Additionally, if you choose -m custom, then you must also specify a custom database amino acid file using -c or --custom_db.

Your input FASTA must also have at least 2 contigs.

Example usage to reorient a number of bacterial chromosomes in input.fasta to begin with the dnaA gene:

dnaapler bulk -i input.fasta -o output_directory_path -t 8  -m chromosome

Usage: dnaapler bulk [OPTIONS]

  Reorients multiple genomes to begin with the same gene

Options:
  -h, --help             Show this message and exit.
  -V, --version          Show the version and exit.
  -i, --input PATH       Path to input file in FASTA format  [required]
  -o, --output PATH      Output directory   [default: output.dnaapler]
  -t, --threads INTEGER  Number of threads to use with BLAST  [default: 1]
  -p, --prefix TEXT      Prefix for output files  [default: dnaapler]
  -f, --force            Force overwrites the output directory
  -e, --evalue TEXT      e value for blastx  [default: 1e-10]
  -m, --mode TEXT        Choose an mode to reorient in bulk. Must be one of:
                         chromosome, plasmid, phage or custom [default:
                         chromosome]
  -c, --custom_db PATH   FASTA file with amino acids that will be used as a
                         custom blast database to reorient your sequence
                         however you want. Must be specified if -m custom is
                         specified.