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#!/bin/bash -e
format=png
mem=1500m
PROGNAME=`basename $0`
function usage {
echo "
USAGE:
create_zoomed_maps.sh -p DIR -c INTEGER -z INTEGER [Options]
DESCRIPTION:
Creates a zoomed map for completed CCT project.
REQUIRED ARGUMENTS:
-p, --project DIR
Path to a completed CCT project.
-c, --center INTEGER
Nucleotide position to center the zoomed map on.
-z, --zoom INTEGER
Zoom multiplier.
OPTIONAL ARGUMENTS:
-f, --format STRING
Image format for output map. Options are png, jpg, svg, svgz.
(Default: png)
-m, --memory STRING
Memory value for Java's -Xmx option (Default: 1500m).
-h, --help
Show this message
EXAMPLE:
create_zoomed_maps.sh -p my_project -c 10000 -z 10 -format svg
"
}
function error_exit {
echo "${PROGNAME}: ${1:-"Unknown Error"}" 1>&2
exit 1
}
function get_filename_without_extension {
basefile=$(basename "$1")
filename=${basefile%.*}
echo $filename
}
function get_path_to_maps {
file="$1"
filename=`echo "$file" | perl -nl -e 'm/(.+)\/cgview_xml\/[^\/]+$/;' -e 'print $1'`
echo $filename
}
function remove_trailing_slash {
string="$1"
new_string=`echo "$string" | perl -nl -e 's/\/+$//;' -e 'print $_'`
echo $new_string
}
while [ "$1" != "" ]; do
case $1 in
-p | --project ) shift
project=$1
;;
-c | --center ) shift
center=$1
;;
-z | --zoom ) shift
zoom=$1
;;
-f | --format ) shift
format=$1
;;
-m | --memory ) shift
mem=$1
;;
-h | --help ) usage
exit
;;
* ) usage
exit 1
esac
shift
done
# The CCT_HOME variable must be set
if [ -z "$CCT_HOME" ]; then
error_exit "Please set the \$CCT_HOME environment variable to the path to the cgview_comparison_tool directory."
fi
cct_home=$CCT_HOME
if [ -z "$project" ]; then
error_exit "Please use '-p' to specify a project. Use '-h' for help."
fi
if [ -z "$center" ]; then
error_exit "Please use '-c' to specify the nucleotide position of interest. Use '-h' for help."
fi
if [ -z "$zoom" ]; then
error_exit "Please use '-z' to specify the zoom multiplier. Use '-h' for help."
fi
if [ -z "$CCT_HOME" ]; then
error_exit "Please set the \$CCT_HOME environment variable to the path to the cgview_comparison_tool directory."
fi
project=`remove_trailing_slash "$project"`
# save and change IFS to avoid problems with filesnames with spaces
OLDIFS=$IFS
IFS=$'\n'
#find all XML files in the project
files=($( find -L "$project" -type f -name "*.xml" ))
# restore IFS
IFS=$OLDIFS
length=${#files[@]}
for (( i=0; i<$length; i++ ));
do
xml_file=${files[$i]}
echo "Generating zoomed map from the file '$xml_file'."
file_no_extension=`get_filename_without_extension "$xml_file"`
path_to_maps=`get_path_to_maps "$xml_file"`
java -jar -Xmx"${mem}" "$cct_home"/bin/cgview.jar -i "$xml_file" -c $center -z $zoom -o "$path_to_maps"/"${file_no_extension}_${center}_${zoom}"."$format" -f "$format"
echo "New map drawn to $path_to_maps/${file_no_extension}_${center}_${zoom}.${format}"
done
|
