document get_maps.sh

README.md

@@ -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

get_maps.sh

 #!/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