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.