Plasmid Database

1. Download plasmid database info file:

ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/plasmids.txt

2. Extract sequences from all accession numbers into a FASTA file using eutils:

''' for i in $(cat plasmids.txt | awk 'BEGIN{FS="\t"} (NR>2) {if ($6 ~ "N") {print $6;} else {print $7}}'); do curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=$i&retmode=text&rettype=fasta"; done > plasmids.fna '''