table of contents
| NAD(1) | User Commands | NAD(1) |
NAME¶
nad - download genome files from NCBI by accession
SYNOPSIS¶
nad [-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.
| June 2020 | nad 0.2.6 |