From 03934e8144c23727c1fbaf8329c645e20e9cf55b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 23 Mar 2021 11:20:58 -0600
Subject: [PATCH] Add USB drive transfer script for ONT GridION

---
 .gitignore          |  1 +
 ont/ont-transfer.sh | 70 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 71 insertions(+)
 create mode 100644 .gitignore
 create mode 100755 ont/ont-transfer.sh

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..9e8bc2d
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+FAP012345
diff --git a/ont/ont-transfer.sh b/ont/ont-transfer.sh
new file mode 100755
index 0000000..fa3988d
--- /dev/null
+++ b/ont/ont-transfer.sh
@@ -0,0 +1,70 @@
+#!/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