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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 data files"
exit 1
fi
data="$1"
shift
data=${data%/}
find "$target" -name "*.e2x" -delete
find "$target" -name "*.e2x.gz" -delete
if [ -f "pubmed001.xml.gz" ]
then
for fl in *.xml.gz
do
base=${fl%.xml.gz}
echo "$base.e2x"
if [ -s "$data/meshtree.txt" ]
then
gunzip -c "$fl" |
xtract -transform "$data/meshtree.txt" -e2index |
gzip -1 > "$target/$base.e2x.gz"
else
gunzip -c "$fl" |
xtract -e2index |
gzip -1 > "$target/$base.e2x.gz"
fi
sleep 1
done
elif [ -f "pubmed001.xml" ]
then
for fl in *.xml
do
base=${fl%.xml}
echo "$base.e2x"
if [ -s "$data/meshtree.txt" ]
then
cat "$fl" |
xtract -transform "$data/meshtree.txt" -e2index |
gzip -1 > "$target/$base.e2x.gz"
else
cat "$fl" |
xtract -e2index |
gzip -1 > "$target/$base.e2x.gz"
fi
sleep 1
done
fi
|
