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slideCheckProcessed.sh
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slideCheckProcessed.sh
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#!/bin/bash
#
# It is good practice to properly name and annotate your script for future reference for
# yourself and others. Trust me, you'll forget why and how you made this!!!
### Creating display functions
### Setting colouring
NONE='\033[00m'
BOLD='\033[1m'
ITALIC='\033[3m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
UNDERLINE='\033[4m'
RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'
### Regarding changing the 'type' of the things printed with 'echo'
### Refer to:
### - http://askubuntu.com/questions/528928/how-to-do-underline-bold-italic-strikethrough-color-background-and-size-i
### - http://misc.flogisoft.com/bash/tip_colors_and_formatting
### - http://unix.stackexchange.com/questions/37260/change-font-in-echo-command
### echo -e "\033[1mbold\033[0m"
### echo -e "\033[3mitalic\033[0m" ### THIS DOESN'T WORK ON MAC!
### echo -e "\033[4munderline\033[0m"
### echo -e "\033[9mstrikethrough\033[0m"
### echo -e "\033[31mHello World\033[0m"
### echo -e "\x1B[31mHello World\033[0m"
function echobold { #'echobold' is the function name
echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic {
echo -e "${ITALIC}${1}${NONE}"
}
function echocyan {
echo -e "${CYAN}${1}${NONE}"
}
function echonooption {
echo -e "${OPAQUE}${RED}${1}${NONE}"
}
# errors
function echoerrorflash {
echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
}
function echoerror {
echo -e "${RED}${1}${NONE}"
}
# errors no option
function echoerrornooption {
echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption {
echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}
### MESSAGE FUNCTIONS
script_copyright_message() {
echo ""
THISYEAR=$(date +'%Y')
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+ The MIT License (MIT) +"
echo "+ Copyright (c) 2016-${THISYEAR} Sander W. van der Laan +"
echo "+ +"
echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +"
echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction, +"
echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
echo "+ subject to the following conditions: +"
echo "+ +"
echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial +"
echo "+ portions of the Software. +"
echo "+ +"
echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT +"
echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +"
echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES +"
echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +"
echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +"
echo "+ +"
echo "+ Reference: http://opensource.org. +"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
script_arguments_error() {
echoerror "$1" # ERROR MESSAGE
echoerror "- Argument #1 -- name of the stain as it appears in the filenames, e.g. FIBRIN."
echoerror "- Argument #2 -- (the path to) the filename, e.g. Image.gct.gz, the script will automatically append STAIN, e.g. STAIN_Image.gct.gz"
echoerror "- Argument #3 -- (the path to) the slideToolkit output directory, e.g. ./slideToolkit"
echoerror "- Argument #4 -- [OPTIONAL] (the path to) the file to compare the processed study numbers with, e.g. ./CompareFile.txt"
echoerror ""
echoerror "An example command would be: slideAppendGCT [arg1: STAIN] [arg2: Image.gct.gz] [arg3: ./slideToolkit] [OPTIONAL arg4: CompareFile.txt]"
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " slideCheckProcessed"
echo ""
echoitalic "* Written by : Tim S. Peters"
echoitalic "* E-mail : [email protected]"
echoitalic "* Last update : 2024-05-20"
echoitalic "* Version : v1.0.0"
echo ""
echoitalic "* Description : This script will collect all study number with a"
echoitalic " correctly processed CellProfiler output."
echoitalic " Additionally, it will compare this list with a given list."
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "Today's: $(date)"
TODAY=$(date +"%Y%m%d") # set Today
echo ""
### REQUIRED | GENERALS
STAIN="$1" # Depends on arg1
RESULTSFILENAME="$2"
OUTDIR="$3"
### OPTIONAL
COMPAREFILE="$4"
if [[ $# -lt 3 ]]; then
echoerrorflash "Oh, computer says no! Number of arguments found $#."
script_arguments_error "You must supply correct (number of) arguments when running *** slideAppendGCT ***!"
else
echo ""
echoitalic "Creating a new log."
echo ""
echoitalic "Collecting data for:"
for filename in $OUTDIR/cp_output/*/"${STAIN}"_"${RESULTSFILENAME}"; do
filedir="$(dirname "$filename")"
echo $filedir | awk -F/ '{print $NF}'
echo $filedir | awk -F/ '{print $NF}' >> $OUTDIR/"${TODAY}"."${STAIN}".processed.study_numbers.log
done
if [ ! $# -eq 0 ]; then
echo "Comparing processed study numbers with given file"
# cat -n $COMPAREFILE $OUTDIR/"${TODAY}"."${STAIN}".processed.study_numbers.log | sort -uk2 | sort -nk1 | cut -f2- > $OUTDIR/"${TODAY}"."${STAIN}".unprocessed_study_numbers.txt
comm -23 <(sort $COMPAREFILE) <(sort $OUTDIR/"${TODAY}"."${STAIN}".processed.study_numbers.log) > $OUTDIR/"${TODAY}"."${STAIN}".unprocessed.study_numbers.log
fi
fi
script_copyright_message