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#!/bin/sh
# Public domain notice for all NCBI EDirect scripts is located at:
# https://www.ncbi.nlm.nih.gov/books/NBK179288/#chapter6.Public_Domain_Notice
if [ "$#" -eq 0 ]
then
echo "Must supply path for indexed files"
exit 1
fi
target="$1"
shift
target=${target%/}
if [ "$#" -eq 0 ]
then
echo "Must supply path for extras files"
exit 1
fi
extras="$1"
shift
extras=${extras%/}
xtras="false"
if [ "$#" -gt 0 ]
then
xtras="$1"
shift
fi
find "$target" -name "*.e2x" -delete
find "$target" -name "*.e2x.gz" -delete
for fl in *.xml.gz
do
base=${fl%.xml.gz}
echo "$base.e2x"
if [ -s "$extras/meshtree.txt" ]
then
gunzip -c "$fl" |
xtract -transform "$extras/meshtree.txt" -e2index "$xtras" |
transmute -format |
gzip -1 > "$target/$base.e2x.gz"
else
gunzip -c "$fl" |
xtract -e2index "$xtras" |
transmute -format |
gzip -1 > "$target/$base.e2x.gz"
fi
sleep 1
done
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