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recursive-gmconvert
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Riccardo PELLARIN
recursive-gmconvert
Commits
676c7e7e
Commit
676c7e7e
authored
Mar 05, 2018
by
samuel hanot
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Plain Diff
update get_maps to use curl instead of links to get cutoff
parent
bd8eaaea
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1
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6 additions
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5 deletions
+6
-5
get_maps.sh
get_maps.sh
+6
-5
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get_maps.sh
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676c7e7e
#!/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
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