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59 lines
1.5 KiB
Julia
59 lines
1.5 KiB
Julia
#!/usr/bin/julia
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# Renames the FASTQ files in a directory by prepending the well number
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# Activate the proper packages
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using Tk
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import XLSX
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using DataFrames
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using Missings
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# Prompt for the folder containing the FASTQs
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fastq_folder = ChooseDirectory()
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# Prompt for the Illumina workbook containing the well info
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illumina_workbook = GetOpenFile()
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# Read in the excel file
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xf = XLSX.readdata(illumina_workbook, "IEM_SampleSheet!B19:D300")
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fastq_ids = DataFrame(xf, :auto)
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rename!(fastq_ids, Symbol.(["SampleId", "RunName", "WellNum"]))
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dropmissing!(fastq_ids)
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fastq_ids = string.(fastq_ids)
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# Get all of the files
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fastqs = readdir(fastq_folder)
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# Iterate through each file
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for fastq in fastqs
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# Get the full path
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fastq_path = joinpath(fastq_folder, fastq)
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# Delete if this is a JSON file
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if last(fastq,5) == ".json"
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rm(fastq_path)
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println(string("Deleting ", fastq_path))
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continue
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end
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# Pull the id based on the file name
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id = first(fastq,21)
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# Find this id in the workbook
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id_row = fastq_ids[fastq_ids.SampleId .== id,:]
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# If there are no matches, keep going
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if size(id_row)[1] < 1
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continue
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end
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# Swap the column and row
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well_num = string(last(id_row.WellNum[1],2), first(id_row.WellNum[1],1))
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# Construct the new filename
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fastq_newname = string(well_num, "_", fastq)
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# Rename the file
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mv(fastq_path, joinpath(fastq_folder, fastq_newname))
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println(string("Renaming ", fastq_path, " to ", joinpath(fastq_folder, fastq_newname)))
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end
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