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nickloman/rsync_ecoli.sh

Created October 29, 2012 15:14
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Retrieve all Escherichia sequences from Genbank with rsync
Raw
rsync_ecoli.sh
rsync -av rsync://ftp.ncbi.nlm.nih.gov/genomes/Bacteria --include "*/" --include "Bacteria/Escherichia*/*.fna" --exclude=* .
# bonus script - concatenate chromosomes and plasmids into single fasta file, make sure the files don't already exist
find . -mindepth 1 -type d | xargs -L 1 -I '{}' find {} -name "*.fna" | while read i ; do cat "$i" >> `dirname "$i"`.fasta ; done
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