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plain)
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#!/bin/sh
for fl in *.xml.gz
do
base=${fl%.xml.gz}
if [ -f "$base.snt" ]
then
continue
fi
if [ -f "$base.xml" ]
then
continue
fi
echo "$fl"
gunzip -c "$fl" | xtract -strict -compress -format flush > "$base.tmp.xml"
xtract -input "$base.tmp.xml" -pattern PubmedArticle -element MedlineCitation/PMID > "$base.uid"
xtract -input "$base.tmp.xml" -unique "$base.uid" -index MedlineCitation/PMID \
-head "<PubmedArticleSet>" -tail "</PubmedArticleSet>" -pattern PubmedArticle > "$base.xml"
rm "$base.tmp.xml"
rm "$base.uid"
touch "$base.snt"
done
|
