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Add USB drive transfer script for ONT GridION

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This commit is contained in:
Thomas A. Christensen II 2021-03-23 11:20:58 -06:00
parent 9735382ac5
commit 03934e8144
Signed by: millironx
GPG key ID: 139C07724802BC5D
2 changed files with 71 additions and 0 deletions
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.gitignore vendored Normal file
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FAP012345

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ont/ont-transfer.sh Executable file
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#!/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 [ "$FOLDERIN" = "" ]; then
if [ -d "fast5_pass" ]; then
FOLDERPATH="$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" = "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+=($(("${WORKING[j]}" + 12)))
done
done
else
KEEPERS=( $(seq "%02g" 01 96) )
fi
# Find where the flash drive is mounted
USBDRIVE=$(mount | grep /media | awk '{print $3}')
# Prompt the users
echo "Extracting FAST5/FASTQ from" "$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