diff --git a/get_maps.sh b/get_maps.sh index ab286d036c39b93011c9a6b0100f48eef76f8c98..0d2f692b186faea2f5fd9b54505beab774276ce5 100755 --- a/get_maps.sh +++ b/get_maps.sh @@ -1,8 +1,9 @@ #!/bin/bash -bindir=$(dirname $0) - +bindir=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) +rec_gmconvert=${bindir}/recursive_gmconvert.sh +echo "rec_gmconvert=${rec_gmconvert}" source ${bindir}/modules.sh for f in $(cat) @@ -10,12 +11,12 @@ do echo $f rsync -a -v -z --delete rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-${f}/ $f cd $f - links http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-$f/analysis > header/map_analysis.txt - cutoff=$(awk '/contour/{print $4}' < header/map_analysis.txt) + curl http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-$f/analysis > header/map_analysis.html + cutoff=$(awk '/contour/{print 3}' < header/map_analysis.html) resolution=$(sed -ne 's/[<>/ ]//g' -ne 's/resolutionByAuthor//gp' header/emd-${f}.xml) echo ${cutoff} > cutoff.txt echo ${resolution} > resolution.txt gunzip -c map/emd_${f}.map.gz > emd_${f}.map - ${bindir}/recursive_gmconvert.sh emd_${f}.map $cutoff $1 $2 + ${rec_gmconvert} -f emd_${f}.map -t $cutoff -n $1 -N $2 cd - done