mirror of
https://github.com/MillironX/sc2-sequencing.git
synced 2024-12-22 11:18:17 +00:00
75 lines
2.3 KiB
Bash
Executable file
75 lines
2.3 KiB
Bash
Executable file
#!/bin/bash
|
|
# Copies fast5 and fastq files from a GridION to the first available USB device
|
|
|
|
# Find the skipped barcodes parameter
|
|
if [[ ${1} = "-s" ]]; then
|
|
OFFSET=${2}
|
|
FOLDERIN=${3}
|
|
else
|
|
echo " Assuming no skipped barcodes"
|
|
echo " CTRL+C if incorrect and call 'ont-transfer -s [1|6|12]', instead"
|
|
OFFSET=1
|
|
FOLDERIN=${1}
|
|
fi
|
|
|
|
# Find the directory we are supposed to copy
|
|
# If no directory was passed, check to see if the current directory will work
|
|
if [[ ! -n "$FOLDERIN" ]]; then
|
|
if [[ -n $(find . -type d -name "fast5_pass") ]]; then
|
|
FOLDERPATH="$PWD"
|
|
FOLDERNAME=$(basename "$PWD")
|
|
else
|
|
echo " ERROR: Can't find FAST5s in current directory and no directory was passed."
|
|
echo " ont-transfer must either be passed a directory or be called from a directory"
|
|
echo " containing a 'fast5_pass' folder containing FAST5 files."
|
|
exit 1
|
|
fi
|
|
else
|
|
FOLDERPATH="$FOLDERIN"
|
|
FOLDERNAME=$(basename "$FOLDERIN")
|
|
fi
|
|
|
|
# Calculate the FASTAs that need copied
|
|
if [[ $OFFSET -gt 1 ]]; then
|
|
if [[ $OFFSET -lt 7 ]]; then
|
|
KEEPERS=(01 02 03 04 05 06)
|
|
else
|
|
KEEPERS=(07 08 09 10 11 12)
|
|
fi
|
|
for ((i = 1; i < 8; ++i)); do
|
|
WORKING=(${KEEPERS[@]: -6})
|
|
for ((j = 0; j < 6; ++j)); do
|
|
KEEPERS+=($(( 10#${WORKING[j]} + 12 )))
|
|
done
|
|
done
|
|
else
|
|
KEEPERS=( $(seq -f "%02g" 01 96) )
|
|
fi
|
|
|
|
# Find where the flash drive is mounted
|
|
# Note that this only works on GridIONs thanks to goofy mounting
|
|
USBDRIVE=$(mount | grep /data | awk '{print $3}' | tail -n1)
|
|
if [[ -n $(echo $USBDRIVE | grep scratch) ]]; then
|
|
echo "No USB drive was detected. Exiting now."
|
|
exit 1
|
|
fi
|
|
|
|
# Prompt the users
|
|
echo "Extracting FAST5/FASTQ from $FOLDERNAME to USB Device $USBDRIVE, skipping after $OFFSET."
|
|
echo "If this is not correct, press CTRL+C within the next 10 seconds to abort..."
|
|
sleep 10
|
|
echo "Proceeding..."
|
|
|
|
# Make output directories
|
|
mkdir -p "$USBDRIVE/$FOLDERNAME/fast5"
|
|
mkdir -p "$USBDRIVE/$FOLDERNAME/fastq"
|
|
|
|
# Copy the files
|
|
for FASTA in ${KEEPERS[@]}; do
|
|
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.gz $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null
|
|
done
|
|
|
|
# Make sure we end on a happy note, regardless if there were actually 96 barcodes
|
|
exit 0
|