Overview

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
2. for file in *.fastq;do new_name=$(echo $file|sed 's/-*//'); mv $file $new_name;done
   • Generic explanation:
   • for "variable name" in "files to consider"; do "new variable name"=$(echo $"variable name"|sed 's/what to find/what to replace/');mv $"new variable name" $"variable name";done

-- DanielDeatherage - 21 Aug 2014