unpack-pubmed


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#!/bin/sh

flags="none"

if [ "$#" -gt 0 ]
then
  flags="$1"
fi

for fl in *.xml.gz
do
  base=${fl%.xml.gz}
  if [ -f "$base.xml" ]
  then
    continue
  fi
  echo "$fl"
  gunzip -c "$base.xml.gz" | xtract -flags "$flags" -unique "$base.uid" -index MedlineCitation/PMID \
    -head "<PubmedArticleSet>" -tail "</PubmedArticleSet>" -pattern PubmedArticle > "$base.xml"
done