I am a microbiologist and new to PowerShell and I have to create a script using zgrep -u

Question

I have a folder of fastq file (genomic sequences) and an excel file with barcodes (series of 20 nucleotides) and I want to search all the barcodes in all fastq files and get the exact matches. I did "zgrep -u barcode file1 file2 file3" individually for few barcodes to test and it works but now I want to create a script that does it for me as I have around 200 different barcodes to look for in 10 files. I am not sure how can I incorporate zgrep into a script like this.

Answer 1

Hello and welcome to stack overflow. I'm very sorry that some people here read over your non-IT background and certainly answer cryptically for you.

About your problem:

First, if possible, install the ImportExcel module on your machine using this PowerShell command:

Install-Module -Name ImportExcel -Scope CurrentUser -Force

After that we can run this small script to execute zgrep for each row in the Excel Document:

# Change this to the path to your file
$FilePath = "C:\Test123.xlsx"

$excelContent = Import-Excel -Path $FilePath
foreach($row in $excelContent)
{
    # Change columnName to the Name of the columne the barcodes are in
    zgrep -u $row.columnName file1 file2 file3
}

This should be all you need for your problem.