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