Commit 4a02f961 authored by samuel hanot's avatar samuel hanot

document get_maps.sh

parent 6e8ec414
......@@ -43,6 +43,28 @@ The script creates a sub-directory (called `i`) for each recursion level `i`, an
Unless you enable serial mode (`-s` flag), all the scripts assume that you are running a cluster with the `slurm` queuing system.
## other scripts:
`get_maps.sh` is used to run a batch of `recursive_gmconvert.sh` on a list of emdb entries. It will fetch the data from the emdb and run the divide-and-conquer GMM calculation.
Example 1: `get_maps.sh -n 2 -N 2 -s <<< 1883`
Example 2: `get_maps.sh -n 2 -N 2 -s < input.txt`
In example 2, `input.txt` contains one emdb entry per line.
### Required arguments:
`-n num_gaussians`: number of gaussians per sub-process
`-N num_iterations`: number of recursion levels
### Optional arguments:
`-s`: enable serial mode
`-h`: display this message
## References
[1] Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps
......
#!/bin/bash
usage() {
echo >&2 \
"usage: get_maps.sh -n num_gaussians -N num_iterations [-s] < input_file.txt
For each emdb entry in input_file.txt, the script downloads it and runs recursive_gmconvert
example:
get_maps.sh -n 2 -N 2 -s <<< 1883
Required arguments:
input_file.txt should contain one emdb entry per line
-n num_gaussians: number of gaussians per sub-process
-N num_iterations: number of recursion levels
Optional arguments:
-s: enable serial mode
-h: display this message"
}
#defaults
n_gaussians=
N=
serial=0
while getopts n:N:sh opt
do
case "$opt" in
n) n_gaussians="$OPTARG";;
N) N="$OPTARG";;
s) serial=1;;
h) usage
exit ;;
\?) # unknown flag
echo >&2 \
usage
exit 1;;
esac
done
#check that necessary options were set
if [[ -z "$n_gaussians" ]] || [[ -z "$N" ]]
then
usage
exit 1
fi
bindir=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
rec_gmconvert=${bindir}/recursive_gmconvert.sh
......
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