nad1
Download genome files from ncbi by accession
Usage
nad [-h]
[-m
nucleotide,protein]
[-e
none,loads,all]
Overview
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.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).