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Merge pull request #201 from pneerincx/master
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Bugfixes for renameFastQs.bash
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@BenjaminsM
BenjaminsM authored Aug 10, 2018
2 parents 9d938dd + 3e27c99 commit 63c304f
Showing 1 changed file with 49 additions and 49 deletions.
98 changes: 49 additions & 49 deletions renameFastQs.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ function _Usage() {
#
# Custom signal trapping functions (one for each signal) required to format log lines depending on signal.
#
function trapSig() {
function _trapSig() {
local _trap_function="${1}"
local _line="${2}"
local _function="${3}"
Expand All @@ -57,23 +57,39 @@ function trapSig() {
done
}

function trapHandler() {
function _trapHandler() {
local _signal="${1}"
local _problematicLine="${2}"
local _function="${3}"
local _exitStatus="${4}"
local _errorMessage="Unknown error in function ${_function}."
_reportFatalError "${_problematicLine}" "${_exitStatus}" "${_errorMessage}"
}

function _reportFatalError() {
local _problematicLine="${1}"
local _exitStatus="${2:-$?}"
local _errorMessage="Unknown error."
_errorMessage="${3:-${_errorMessage}}"
#
# Notify on STDOUT.
#
echo "
$(hostname) - ${SCRIPT_NAME}:${_problematicLine}: FATAL: exit code = ${_exitStatus}
$(hostname) - ${SCRIPT_NAME}:${_problematicLine}: error message = ${_errorMessage}
$(hostname) - ${SCRIPT_NAME}:${_problematicLine}: FATAL: exit code = ${_exitStatus}
$(hostname) - ${SCRIPT_NAME}:${_problematicLine}: error message = ${_errorMessage}
"
#
# Reset trap and exit.
#
trap - EXIT
exit 1
}


#
# Trap all exit signals: HUP(1), INT(2), QUIT(3), TERM(15), ERR
#
trapSig 'trapHandler' '${LINENO}' '${FUNCNAME:-main}' '$?' HUP INT QUIT TERM EXIT ERR

_trapSig '_trapHandler' '${LINENO}' '${FUNCNAME:-main}' '$?' HUP INT QUIT TERM EXIT ERR

function _RenameFastQ() {
local _fastqPath="${1}"
Expand All @@ -96,29 +112,9 @@ function _RenameFastQ() {
local _fastqFile="$(basename "${_fastqPath}")"

#
# Do NOT parse filenames: get the essential stuff from the sequence read IDs instead
# Get essential meta-data from the sequence read IDs in the FastQ file.
# (Do NOT rely on parsing FastQ filenames!)
#
#local _regex='^([A-Z0-9]*XX)_(103373-[0-9][0-9]*-[0-9][0-9]*)_([ATCG][ATCG]*-[ATCG][ATCG]*)_L00([1-8])_R([12]).fastq.gz$'
#if [[ "${_fastqFile}" =~ ${_regex} ]]
#then
# local _flowcell="${BASH_REMATCH[1]}"
# local _customerBatchSampleCombi="${BASH_REMATCH[2]}"
# local _barcodes="${BASH_REMATCH[3]}"
# local _lane="${BASH_REMATCH[4]}"
# local _sequenceReadOfPair="${BASH_REMATCH[5]}"
# if [[ "${enableVerboseLogging}" -eq 1 ]]
# then
# echo "DEBUG: Found _flowcell ............... = ${_flowcell}"
# echo "DEBUG: Found _customerBatchSampleCombi = ${_customerBatchSampleCombi}"
# echo "DEBUG: Found _barcodes ............... = ${_barcodes}"
# echo "DEBUG: Found _lane ................... = ${_lane}"
# echo "DEBUG: Found _sequenceReadOfPair ..... = ${_sequenceReadOfPair}"
# fi
#else
# echo "FATAL: Failed to parse filename for ${_fastq}"
# exit 1
#fi

local _firstReadID=$(zcat "${_fastqPath}" | head -1)
if [[ "${enableVerboseLogging}" -eq 1 ]]
then
Expand All @@ -142,8 +138,7 @@ function _RenameFastQ() {
#
if [[ "${#_run}" -lt 3 ]]
then
echo "FATAL: run number detected in ID of first read is too short (< 3): ${_run}"
exit 1
_reportFatalError ${LINENO} '1' 'Run number detected in ID of first read is too short (< 3): '"${_run}."
elif [[ "${#_run}" -eq 3 ]]
then
_run="0${_run}"
Expand All @@ -157,8 +152,7 @@ function _RenameFastQ() {
echo "DEBUG: Found _sequenceReadOfPair ..... = ${_sequenceReadOfPair}"
fi
else
echo "FATAL: Failed to parse required meta-data values from ID of first read of ${_fastqPath}"
exit 1
_reportFatalError ${LINENO} '1' "Failed to parse required meta-data values from ID of first read of ${_fastqPath}".
fi

#
Expand All @@ -185,13 +179,15 @@ function _RenameFastQ() {
fi
elif [[ "${_mostAbundandBarcode}" =~ N ]]
then
echo "ERROR: Most abundant barcode(s) in max 1000 reads from middle of FastQ contains Ns: ${_barcodes}"
qualityControl='failed'
echo "ERROR: Most abundant barcode(s) in max 1000 reads from middle of FastQ contains Ns: ${_mostAbundandBarcode}."
echo "ERROR: Skipping discarded FastQ ${_fastqFile} due to poor sequencing quality of barcode(s)."
return
else
echo "ERROR: Failed to determine the most abundant barcode(s) from max 1000 reads from middle of FastQ."
echo "FATAL: Failed to process FastQ ${_fastqFile} due to poor sequencing quality of barcode(s)."
exit 1
qualityControl='failed'
echo "ERROR: Failed to determine the most abundant barcodes from max 1000 reads from middle of FastQ."
echo "ERROR: Failed to parse barcode(s) from read IDs of FastQ file ${_fastqFile}."
return
fi

local _fastqChecksum=$(cat "${_fastqDir}/"*.md5 | grep "${_fastqFile}" | awk '{print $1}')
Expand All @@ -208,9 +204,7 @@ function _RenameFastQ() {
#
if [[ -e "${_newFastqDir}/${_newFastqFile}" ]]
then
echo "FATAL: ${_newFastqDir}/${_newFastqFile} already exists."
echo "FATAL: will NOT move ${_fastqPath} -> ${_newFastqDir}/${_newFastqFile}."
exit 1
_reportFatalError ${LINENO} '1' "${_newFastqDir}/${_newFastqFile} already exists; will NOT move ${_fastqPath} -> ${_newFastqDir}/${_newFastqFile}."
fi

#
Expand All @@ -233,7 +227,7 @@ function _RenameFastQ() {
enableVerboseLogging=0 # Disabled by default.
while getopts "s:f:hv" opt
do
case $opt in
case ${opt} in
h)
_Usage
#
Expand All @@ -252,10 +246,10 @@ do
enableVerboseLogging=1
;;
\?)
_reportError ${LINENO} '1' "Invalid option -${OPTARG}. Try \"$(basename $0) -h\" for help."
_reportFatalError "${LINENO}" '1' "Invalid option -${OPTARG}. Try \"$(basename $0) -h\" for help."
;;
:)
_reportError ${LINENO} '1' "Option -${OPTARG} requires an argument. Try \"$(basename $0) -h\" for help."
_reportFatalError "${LINENO}" '1' "Option -${OPTARG} requires an argument. Try \"$(basename $0) -h\" for help."
;;
esac
done
Expand All @@ -266,15 +260,15 @@ done
shift $(($OPTIND - 1))
if [[ ! -z ${1:-} ]]
then
_reportError ${LINENO} '1' "Invalid argument \"$1\". Try \"$(basename $0) -h\" for help."
_reportFatalError "${LINENO}" '1' "Invalid argument \"$1\". Try \"$(basename $0) -h\" for help."
fi

#
# Check if required args are present.
#
if [[ -z "${sequencingStartDate:-}" || -z "${fastqFilePattern:-}" ]]
then
_reportError ${LINENO} 1 "One ore more required arguments is missing. Try \"$(basename $0) -h\" for help."
_reportFatalError "${LINENO}" '1' "One ore more required arguments is missing. Try \"$(basename $0) -h\" for help."
fi

#
Expand All @@ -285,20 +279,26 @@ if [[ "${sequencingStartDate}" =~ ${ssd_regex} ]]
then
echo "INFO: Using sequencingStartDate ${sequencingStartDate}"
else
_reportError ${LINENO} 1 "sequencingStartDate in unsupported format. Must be YYMMDD, but got ${sequencingStartDate}."
_reportFatalError "${LINENO}" '1' "sequencingStartDate in unsupported format. Must be YYMMDD, but got ${sequencingStartDate}."
fi

#
# Process FastQ files.
#
qualityControl='unknown'
for FastQ in $(ls -1 ${fastqFilePattern})
do
_RenameFastQ "${FastQ}" "${sequencingStartDate}"
done

#
# Reset trap and exit.
# Reset trap and exit with 0 or 1 depending on wether QC was Ok or failed.
#
echo "INFO: Finished successfully!"
trap - EXIT
exit 0
if [[ "${qualityControl}" == 'failed' ]]
then
_reportFatalError "${LINENO}" '1' "One or more FastQ files failed QC and was not renamed!."
else
echo "INFO: Finished successfully!"
trap - EXIT
exit 0
fi

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