This page is designed to give minor examples, and general principles for renaming multiple files at once from the command line based on given criteria and wildcards. Makes use of a command line for loop and the sed command.

Renaming multiple fastq files

  1. Assume you have downloaded multiple fastq files which are of format: Samplename-Lane-runID-etc-etc.fastq ... the following command will rename all files to Samplename.fastq.
  2. for f in *.fastq;do new_name=$(echo $file|sed 's/-*/.fastq/'); mv -i $file $new_name;done
    • Generic explanation in parts:
    • for f in *.fastq;
      • "for" is the start of a for loop which allows you to do the same thing to multiple files sequentially
      • generate a generic variable named "f" which is a list of all files in the current directory that end in ".fastq"
    • do new_name=$(echo $file|
      • do is what you want to do with each of the entries in the for loop
      • generate a new variable named "new name" with the starting point of the old file name, change the name based on the following sed command.

    • do "new variable name"=$(echo $"variable name"|sed 's/what to find/what to replace/');mv $"new variable name" $"variable name";done

-- Main.DanielDeatherage - 21 Aug 2014

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Topic revision: r3 - 27 Aug 2014 - 17:08:45 - Main.DanielDeatherage
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