ProtocolsMassRename < Lab

---+ Overview

This is an example command for renaming multiple files at once. Ideally it is presented as a method for shortening file names by removing common elements in the name. It could similarly be used to create backup copies of a file to play with by changing the "mv" command to a "cp" command. This command works as a single line command on linux/unix, and should be entered directly into the command prompt.

---+ Renaming multiple fastq files

   * 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:
   * for f in *.fastq;do new_name=$(echo $file|sed 's/-*/.fastq/'); mv -i $file $new_name;done
      * Generic explanation in parts:
      * for f in *.fastq;
         * "for" is the start of a for loop which allows you to do the same thing to multiple files sequentially 
         * generate a generic variable named "f" which is a list of all files in the current directory that end in ".fastq"
         * ; end the existing for loop generation
      * do new_name=$(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.
      * sed 's/-*/.fastq/');
         * "sed" is the name of the command to be called. it is effectively just a find and replace command. It has 3 parts separated by / marks, as follows:
            * "s" tells the command you are dealing with a string
            * "-*" says match everything after and including the first hyphen, change this according to the particular sample so you are sure that it is only matching what you want it to
            * ".fastq" says what you want to replace the matched text with
            * ; break apart the next command as if it were being executed on its own line
      * mv -i $file $new_name
         * "mv -i" is being used as a rename command here, with the -i flag meaning not to overwrite existing file name. This is important if your replacement string is wrong and you are generating multiple final names that are identical.
         * $file $new_name this uses the previously created in line variables to reference the existing file as well as the new name you want to name the file.
      * ;done
         * all for loops end with a "done" command



-- Main.DanielDeatherage - 21 Aug 2014
This topic: Lab > ComputationList > ProtocolsMassRename
Topic revision: r5 - 2014-09-09 - DanielDeatherage