ncbi-acc-download - download genome files from NCBI by
accession
ncbi-acc-download [-h] [-m {nucleotide,protein}] [-e
{none,loads,all}]
Script to download sequences from GenBank/RefSeq by accession
through the NCBI ENTREZ API.
[-F {fasta,genbank,featuretable,gff3}] [-o OUT] [-p PREFIX] [-r]
[--url] [-v] NCBI-accession [NCBI-accession ...]
- -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.
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.