NCBI-ACC-DOWNLOAD

NAME

ncbi-acc-download - download genome files from NCBI by accession

SYNOPSIS

ncbi-acc-download [-h] [-m {nucleotide,protein}] [-e {none,loads,all}]

DESCRIPTION

Script to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.

OPTIONS

[-F {fasta,genbank,featuretable,gff3}] [-o OUT] [-p PREFIX] [-r] [--url] [-v] NCBI-accession [NCBI-accession ...]

positional arguments:

NCBI-accession

optional arguments:

-h, --help

show this help message and exit

-m {nucleotide,protein}, --molecule {nucleotide,protein}

Molecule type to download. Default: nucleotide

-e {none,loads,all}, --extended-validation {none,loads,all}

Perform extended validation. Possible options are ’none’ to skip validation, ’loads’ to check if the sequence file loads in Biopython, or ’all’ to run all checks. Default: none

-F {fasta,genbank,featuretable,gff3}, --format
{fasta,genbank,featuretable,gff3}

File format to download nucleotide sequences in. Default: genbank

-o OUT, --out OUT

Single filename to use for the combined output.

-p PREFIX, --prefix PREFIX

Filename prefix to use for output files instead of using the NCBI ID.

-r, --recursive

Recursively get all entries of a WGS entry.

--url

Instead of downloading the sequences, just print the URLs to stdout.

-v, --verbose

Print a progress indicator.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.