#! /bin/bash
# Last edited on 2008-06-15 08:22:05 by stolfi

# Usage: "ncbi_fetch ${outDir} ${id}
# Fetches the NCBI file "${id}" in Genbank format.
# Puts it in ${outDir}/${id}
# The ${id} may or may not include include a version number,
# e.g. "NC_003076.5".

# Parse command line args
if [[ $# -ne 2 ]]; then  echo "wrong nargs" 1>&2 ; fi
outDir="$1"; shift
id="$1"; shift

# Fetch the data
ofile="${outDir}/${id}"
ncbi="http://www.ncbi.nlm.nih.gov/entrez/viewer.cgi"

# Example URL:
# 'http://www.ncbi.nlm.nih.gov/entrez/viewer.cgi?db=nucleotide&val=NC_005789.1&save=on&view=gb'

echo "=== ${ofile} ==="
mkdir -p ${outDir}/${sp}
wget -nv "${ncbi}?db=nucleotide&val=${id}&save=on&view=gbwithparts" -O ${ofile}
ls -l ${ofile}
head -5 ${ofile}
echo "..."
tail -5 ${ofile}