Create ONT renaming script

ont/Project.toml

@@ -0,0 +1,10 @@
+name = "ONTRename"
+uuid = "e92456f0-0b2d-4004-b474-3ee287651c88"
+authors = ["Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>"]
+version = "0.1.0"
+
+[deps]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Missings = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
+Tk = "4225ea8a-3324-57e7-9ddc-5798a2cb9eab"
+XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"

ont/README.md

@@ -8,18 +8,6 @@ contain some "faults" to work around these idiosyncrasies.
 
 ## Usage
 
-### `ont-demux`
-
-```bash
-ont-demux FAP_FOLDER
-```
-
-Consolidates all FAST5s into a single gzipped FASTQ using ONT's
-`guppy_barcoder`. Note that this is for MinKNOW's default settings of 4000
-reads/file. It is _highly_ recommended to set the "Number of Reads per File"
-entry in MinKNOW to 0, and checking "Compress FASTQs" to produce nearly the same
-results.
-
 ### `ont-transfer`
 
 ```bash
@@ -29,11 +17,43 @@ ont-transfer [-s 1|6|12] FAP_FOLDER
 Transfers all of the passing FAST5 and FASTQ files to the first available USB
 drive, skipping empty barcodes based on the number of the first skip passed
 through the `-s` parameter, consolidating all files of the same type into one
-folder for easier sorting and uploading.
+folder for easier sorting and uploading, and concatenating and compressing FASTQ
+files into one per barcode.
+
+### `ont-rename.jl`
+
+To be run with Julia.
+
+```powershell
+julia --project=PATH_TO_ONT_FOLDER PATH_TO_ONT-RENAME.jl
+```
+
+In practice, this looks like
+
+```powershell
+julia --project=C:\Users\MillironX\ont C:\Users\MillironX\illumina\ont-rename.jl
+```
+
+### `ont-demux` (deprecated)
+
+```bash
+ont-demux FAP_FOLDER
+```
+
+**This functionality is now wrapped into `ont-Transfer`, which can produce the
+same results using far fewer resources and in far less time.**
+
+Consolidates all FAST5s into a single gzipped FASTQ using ONT's
+`guppy_barcoder`. Note that this is for MinKNOW's default settings of 4000
+reads/file. It is _highly_ recommended to set the "Number of Reads per File"
+entry in MinKNOW to 0, and checking "Compress FASTQs" to produce nearly the same
+results.
 
 ## Installation
 
-### Requirements
+### `ont-transfer` and `ont-demux`
+
+#### Requirements
 
 - git
 - guppy (Get from [ONT Community](https://nanoporetech.com/community)
@@ -46,7 +66,7 @@ a terminal and running
 sudo apt-get install git parallel -y
 ```
 
-### Instructions
+#### Instructions
 
 Open a terminal (Ctrl+Alt+T), and use the following commands
 
@@ -58,3 +78,25 @@ cp wphl-bioinformatics/ont/* ~/bin
 chmod +x ~/bin/*
 source ~/.bashrc
 ```
+
+### `ont-rename`
+
+These scripts require [Julia](https://julialang.org).
+
+1. Download and install Julia
+    1. Select "Add Julia to PATH" as an option
+    2. All other default options will work
+2. Download the Repo's ZIP file (click green button on upper-right)
+3. Press `Win+R`, type `%USERPROFILE%` and press Enter
+4. Copy the ont folder from the ZIP file into the newly opened folder
+5. Press `Win+X`, then `I` to open a new PowerShell window
+6. Type `julia --project=$env:USERPROFILE\ont` and press Enter
+7. Press the `]` key, the prompt should change to say `(ONTRename) pkg>`
+8. Run `instantiate`
+9. Press the backspace key to return to the `julia>` prompt
+10. Run `exit()`
+11. Close PowerShell
+12. Right-click the Windows desktop, and click "New | Shortcut..."
+13. Type `julia --project=%USERPROFILE%\ont
+    %USERPROFILE%\ont\ont-rename.jl` and click Next
+14. Type `Rename ONT FASTQs` or something else memorable and click "Finish"

ont/ont-rename.jl

@@ -0,0 +1,87 @@
+#!/usr/bin/julia
+# Renames the FASTQ files in a directory by prepending the well number based on
+# a MiSeq run workbook
+
+# Activate the proper packages
+using Tk
+import XLSX
+using DataFrames
+using Missings
+
+# Prompt for the folder containing the FASTQs
+fastq_folder = ChooseDirectory()
+
+# Prompt for the Illumina workbook containing the well info
+ont_workbook = GetOpenFile()
+
+# Read in the excel file
+xf = XLSX.readdata(ont_workbook, "Run Worksheet!B9:D56")
+fastq_ids = DataFrame(xf, :auto)
+rename!(fastq_ids, Symbol.(["SampleId", "Taxa", "Barcode"]))
+dropmissing!(fastq_ids)
+fastq_ids = string.(fastq_ids)
+
+# Truncate the barcode number
+fastq_ids.Barcode = last.(fastq_ids.Barcode, 2)
+
+# Get all of the files
+fastqs = readdir(fastq_folder)
+
+# Find the FAP number somewhere in the excel workbook
+# (The workbooks are not very uniform, so we need to go hunting)
+fap_search = XLSX.readdata(ont_workbook, 1, "D1:K20")
+fap_search = string.(skipmissing(fap_search))
+fap_xl = ""
+for fap in fap_search
+    global fap_xl
+    if first(fap, 3) == "FAP"
+        fap_xl = fap
+        continue
+    end
+end
+
+# Check if the FAP numbers from the directory and the Excel workbook match
+fap_fl = split(fastqs[1], "_")[1]
+if fap_fl != fap_xl
+    # Yikes! They don't match! Check if the user is ok with that
+    proceed = Messagebox(message=string(fap_fl,
+                                        " from the file system doesn't match ",
+                                        fap_xl,
+                                        " from the workbook. ",
+                                        "You might be renaming the wrong files. ",
+                                        "Rename anyway?"))
+
+    # The user clicked "cancel"
+    if proceed == "cancel"
+        exit()
+    end
+
+end
+
+# Iterate through each file
+for fastq in fastqs
+    # Get the full path
+    fastq_path = joinpath(fastq_folder, fastq)
+
+    # Pull the barcode number and FAP number based on the file name
+    # The file name is divided into 5 chucks separated by underscores,
+    # The barcode number is the last two characters of the third chunk
+    FAP = split(fastq, "_")[1]
+    bc = last(split(fastq, "_")[3], 2)
+
+    # Find this id in the workbook
+    id_row = fastq_ids[fastq_ids.Barcode .== bc,:]
+
+    # If there are no matches, keep going
+    if size(id_row)[1] < 1
+        continue
+    end
+
+    # Construct the new filename
+    fastq_newname = string(FAP, "_pass_", id_row.SampleId[1], ".fastq.gz")
+
+    # Rename the file
+    mv(fastq_path, joinpath(fastq_folder, fastq_newname))
+    println(string("Renaming ", fastq_path, " to ", joinpath(fastq_folder, fastq_newname)))
+
+end

ont/src/ONTRename.jl

@@ -0,0 +1 @@
+# This file intentionally empty