Command Line Interface Reference

seqbank

seqbank [OPTIONS] COMMAND [ARGS]...

Options

--install-completion: Install completion for the current shell.

--show-completion: Show completion for the current shell, to copy it or customize the installation.

add

Add sequences from a file or list of files to a SeqBank.

Args:: path (Path): The path to the SeqBank. files (list[Path]): A list of file paths containing sequences. format (str, optional): The format of the sequence files. Defaults to “”. filter (Path, optional): A filter file for sequences. Defaults to None.

seqbank add [OPTIONS] PATH FILES...

Options

--format <format>

Default:

--filter <filter>

Arguments

PATH: Required argument <click.types.Path object at 0x7f9670b2b690>

FILES: Required argument(s) <click.types.Path object at 0x7f966f5c4510>

add-sequence-from-file

Add a sequence from a file with a single sequence to a SeqBank.

Args:: path (Path): The path to the SeqBank. files (list[Path]): A list of file paths containing sequences. format (str, optional): The format of the sequence files. Defaults to “”. filter (Path, optional): A filter file for sequences. Defaults to None.

seqbank add-sequence-from-file [OPTIONS] PATH ACCESSION FILE

Options

--format <format>

Default:

Arguments

PATH: Required argument <click.types.Path object at 0x7f9670b6fb90>

ACCESSION: Required argument STRING

FILE: Required argument <click.types.Path object at 0x7f96718720d0>

count

Display the number of accessions in a SeqBank.

Args:: path (Path): The path to the SeqBank.

seqbank count [OPTIONS] PATH

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715de990>

cp

Copy each sequence from one SeqBank to another.

Args:: path (Path): The path to the source SeqBank. new (Path): The path to the destination SeqBank.

seqbank cp [OPTIONS] PATH NEW

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715de590>

NEW: Required argument <click.types.Path object at 0x7f96715de110>

delete

Delete sequences from a SeqBank.

Args:: path (Path): The path to the SeqBank. accessions (list[str]): A list of accessions to delete from the SeqBank.

seqbank delete [OPTIONS] PATH ACCESSIONS...

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715dfdd0>

ACCESSIONS: Required argument(s) STRING

dfam

Download DFam sequences to a SeqBank.

Args:: path (Path): The path to the SeqBank. release (str, optional): The DFam release version to download. Defaults to “current”. curated (bool, optional): Whether to download curated sequences. Defaults to True.
Returns:: bool: True if the download and addition were successful, False otherwise.

seqbank dfam [OPTIONS] PATH

Options

--release <release>

Default:: current

--curated, --no-curated

Default:: True

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715df990>

export

Export a SeqBank to a specified format.

Args:: path (Path): The path to the SeqBank. output (Path): The path to save the exported sequences. format (str, optional): The format for the exported sequences. Defaults to “fasta”.

seqbank export [OPTIONS] PATH OUTPUT

Options

--format <format>

Default:: fasta

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715de290>

OUTPUT: Required argument <click.types.Path object at 0x7f96715dcf90>

histogram

Generate a histogram of sequence lengths from a SeqBank.

Args:: path (Path): The path to the SeqBank. output_path (Path, optional): The path to save the histogram. If None, the histogram will be displayed. show (bool, optional): Whether to display the histogram. Defaults to False. nbins (int, optional): The number of bins for the histogram. Defaults to 30.

seqbank histogram [OPTIONS] PATH

Options

--output-path <output_path>

--show, --no-show

Default:: False

--nbins <nbins>

Default:: 30

--min <min>

Default:: 0

--max <max>

Default:: 0

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715dc950>

ls

List accessions in a SeqBank.

Args:: path (Path): The path to the SeqBank.

seqbank ls [OPTIONS] PATH

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715de890>

refseq

Download all RefSeq sequences to a SeqBank.

Args:: path (Path): The path to the SeqBank. max (int, optional): Maximum number of sequences to add. Defaults to 0 (all). workers (int, optional): Number of workers to use for downloading. Defaults to -1. tmp_dir (Path, optional): Temporary directory for downloads. Defaults to None.

seqbank refseq [OPTIONS] PATH

Options

--max <max>

Default:: 0

--workers <workers>

Default:: -1

--tmp-dir <tmp_dir>

Arguments

PATH: Required argument <click.types.Path object at 0x7f96715dfb50>

url

Add sequences from a list of URLs to a SeqBank.

Args:: path (Path): The path to the SeqBank. urls (list[str]): A list of URLs containing sequences. format (str, optional): The format of the sequence files. Defaults to “”. max (int, optional): Maximum number of sequences to add. Defaults to 0 (all). workers (int, optional): Number of workers to use for downloading. Defaults to -1. tmp_dir (Path, optional): Temporary directory for downloads. Defaults to None.

seqbank url [OPTIONS] PATH URLS...

Options

--format <format>

Default:

--max <max>

Default:: 0

--workers <workers>

Default:: -1

--tmp-dir <tmp_dir>

Arguments

PATH: Required argument <click.types.Path object at 0x7f9670b67610>

URLS: Required argument(s) STRING