utils to download, manipulate NCBI data
1 genome-download
dependencies:
# cpanm Cwd
# wget https://github.com/brentp/gargs/releases/download/v0.3.8/gargs_linux -o /usr/bin/gargs
command line interface:
$ genome-download
Usage:
genome-download <genome_list> <type:fna|gff|faa> <db>
Example: genome-download gcf.txt fna GCF
VERSION: 0.0.1
The gcf.txt can be parsed from NCBI assembly report file:
grep -P -v ^"#" assembly_summary_refseq.txt | cut -f20 | grep -w -v "na" >gcf.txt