plot_DRISEE_shell.sh

#!/bin/sh

#written 10-18-11
if [ $# -lt 2 ]                                                                                     # usage and exit if 4 args are not supplied
then
    echo "plot_DRISEE_shell.sh"
    echo "A shell script to plot linear graphs from *.DRISEE or *.DRISEE.per files (DRISEE analysis outputs)"
    echo
    echo "USAGE: >plot_DRISEE_shell.sh <file_in> <bps_indexed>"
    echo   
    echo "     <file_in>         : no default    :: (string) name of the input file (tab delimited file) assumes *.DRISEE or *.DRISEE.per and converts"
    echo "     <image_type>      : dafault = pdf :: (string)  type of image - can choose pdf or png" 
    echo "     <bps_indexed>     : default = 1   :: (int)     0|1 does the input file contain bp index"
    echo
    echo "NOTE: This script requires a copy of plot_DRISEE.11-19-12.r to be placed in your /usr/bin/ directory"
    echo
    echo "Citation:" 
    echo "     Keegan KP, Trimble WL, Wilkening J, Wilke A, Harrison T, et al. (2012)"
    echo "     A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE." 
    echo "     PLoS Comput Biol 8(6): e1002541. doi:10.1371/journal.pcbi.1002541"  
    echo
    exit 1
fi

time_stamp=`date +%m-%d-%y_%H:%M:%S:%N`;  # create the time stamp month-day-year_hour:min:sec:nanosec

FILE_IN=$1
IMAGETYPE=$2
BPSINDEXED=$3

# set variable defaults
: ${IMAGETYPE:="pdf"} # set default value for image_type
: ${BPSINDEXED:=1} # set default value for bps_indexed


# perl ~/bin/STAT_to_R.pl -input_file $1 -output_pattern $1;

# drisee_stat_file=$1".PERCENT_COUNTS";

echo "# script generated by plot_DRISEE_shell.sh to run plot_pco.r" >> plot_DRISEE_script.$time_stamp.r
echo "# time stamp; $time_stamp" >> plot_DRISEE_script.$time_stamp.r
echo "source(\"~/bin/plot_DRISEE.11-28-12.r\")" >> plot_DRISEE_script.$time_stamp.r
#echo "plot_DRISEE(file_in = \"$1\", bps_indexed = \"$2\")" >> plot_DRISEE_script.$time_stamp.r
#echo "plot_DRISEE(file_in = \"$drisee_stat_file\", bps_indexed = \"$2\")" >> plot_DRISEE_script.$time_stamp.r
echo "plot_DRISEE(file_in = \"$FILE_IN\", image_type  = \"$IMAGETYPE\", bps_indexed = \"$BPSINDEXED\")" >> plot_DRISEE_script.$time_stamp.r

R --vanilla --slave < plot_DRISEE_script.$time_stamp.r

#if [ -e plot_DRISEE_script.$time_stamp.r ]
#then
   # rm plot_DRISEE_script.$time_stamp.r
  
#fi