sh 从wormbase基因组序列生成blast基因组

Posted 2021-05-07

# Download ref genomes/contigs
lftp ftp.wormbase.org -e 'mget /pub/wormbase/species/**/sequence/genomic/*.current.genomic.fa.gz'

function get_genomes() {
    for i in `ls -1 *canonical*fa.gz`; do
        IFS='.' read -r -a genome <<< "$i";
        zcat ${i} | sed "s/>/> ${genome[0]} :: /g" 
    done;
}

get_genomes() |  makeblastdb -in - -out wormbase_blast_genome -title wormbase_blast -dbtype=nucl