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Merge branch 'master' of https://github.com/MillironX/wphl-bioinformatics

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This commit is contained in:
Thomas A. Christensen II 2021-03-26 14:05:08 -06:00
commit adf52e1e71
1 changed files with 10 additions and 9 deletions
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19
ont/ont-transfer.sh → ont/ont-transfer
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@ -14,7 +14,7 @@ fi
# Find the directory we are supposed to copy # Find the directory we are supposed to copy
# If no directory was passed, check to see if the current directory will work # If no directory was passed, check to see if the current directory will work
if [[ -n "$FOLDERIN" = "" ]]; then if [[ ! -n "$FOLDERIN" ]]; then
if [[ -n $(find . -type d -name "fast5_pass") ]]; then if [[ -n $(find . -type d -name "fast5_pass") ]]; then
FOLDERPATH="$PWD" FOLDERPATH="$PWD"
FOLDERNAME=$(basename "$PWD") FOLDERNAME=$(basename "$PWD")
@ -30,16 +30,16 @@ else
fi fi
# Calculate the FASTAs that need copied # Calculate the FASTAs that need copied
if [[ "$OFFSET" -gt 1 ]]; then if [[ $OFFSET -gt 1 ]]; then
if [[ "$OFFSET" -lt 7 ]]; then if [[ $OFFSET -lt 7 ]]; then
KEEPERS=(01 02 03 04 05 06) KEEPERS=(01 02 03 04 05 06)
else else
KEEPERS=(07 08 09 10 11 12) KEEPERS=(07 08 09 10 11 12)
fi fi
for ((i = 1; i < 8; ++i)); do for ((i = 1; i < 8; ++i)); do
WORKING=("${KEEPERS[@]: -6}") WORKING=(${KEEPERS[@]: -6})
for ((j = 0; j < 6; ++j)); do for ((j = 0; j < 6; ++j)); do
KEEPERS+=($(("${WORKING[j]}" + 12))) KEEPERS+=($(( 10#${WORKING[j]} + 12 )))
done done
done done
else else
@ -47,14 +47,15 @@ else
fi fi
# Find where the flash drive is mounted # Find where the flash drive is mounted
USBDRIVE=$(mount | grep /media | awk '{print $3}') # Note that this only works on GridIONs thanks to goofy mounting
if [[ -n "$USBDRIVE" ]]; then USBDRIVE=$(mount | grep /data | awk '{print $3}' | tail -n1)
if [[ -n $(echo $USBDRIVE | grep scratch) ]]; then
echo "No USB drive was detected. Exiting now." echo "No USB drive was detected. Exiting now."
exit 1 exit 1
fi fi
# Prompt the users # Prompt the users
echo "Extracting FAST5/FASTQ from" "$FOLDERNAME" "to USB Device $USBDRIVE, skipping after" "$OFFSET""." echo "Extracting FAST5/FASTQ from $FOLDERNAME to USB Device $USBDRIVE, skipping after $OFFSET."
echo "If this is not correct, press CTRL+C within the next 10 seconds to abort..." echo "If this is not correct, press CTRL+C within the next 10 seconds to abort..."
sleep 10 sleep 10
echo "Proceeding..." echo "Proceeding..."
@ -64,7 +65,7 @@ mkdir -p "$USBDRIVE/$FOLDERNAME/fast5"
mkdir -p "$USBDRIVE/$FOLDERNAME/fastq" mkdir -p "$USBDRIVE/$FOLDERNAME/fastq"
# Copy the files # Copy the files
for FASTA in "${KEEPERS[@]}"; do for FASTA in ${KEEPERS[@]}; do
cp -n $FOLDERPATH/*/fast5_pass/barcode$FASTA/*.fast5 $USBDRIVE/$FOLDERNAME/fast5 2> /dev/null cp -n $FOLDERPATH/*/fast5_pass/barcode$FASTA/*.fast5 $USBDRIVE/$FOLDERNAME/fast5 2> /dev/null
cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null
cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq.gz $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq.gz $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null