Sign in to follow this  
Followers 0

Batch Command Help

2 posts in this topic

Hi Guys,

I would like to run fastq-dump software (it changes format of DNA sequencing data) and repeat it (when the last process is complete) until all the .sra files in a directory are reformatted to fastq.

I have downloaded a study and the sra files are organize in a series of folders: SRP*\SRS*\SRX*\SRR*\SRA*.sra

I can easily put all the sra files into one folder (if needed) but I can't make fastq-dump do anything more than one-at-time conversion.

For example, currently I am using for the file SRRXXXXX1.sra in the same folder as the fastq-dump app:

fastq-dump --split-files --gzip SRRXXXXX1.sra

I get SRRXXXX1.fastq.gzip but SRRXXXXX2.sra is left alone.

Please help me with batching the conversion!

I wish I could run: fastq-dump --split-files --gzip *.sra

or fastq-dump --split-files --gzip SRP*\SRS*\SRX*\SRR*\SRA*.sra

but it doesn't appear fastq-dump supports *.sra

I am inept at batching files. I just need simple code to run fastq-dump --split-files --gzip SRXXXXX1.sra

and repeat for every single .sra file when the last file is completed (can't do at the same time, it's 200G of data).

This is for windows 7 64 bit.


Edited by Adjuvant

Share this post

Link to post
Share on other sites

I'd use find from linux to get all absolute path name of *.sra files. You can find a native win32 port there and the download link is there.

The find.exe would be stored in "c:\batch" for example.

The files to process would be stored in the folder "C:\SEQ"

Then the batch would be pretty easy:

c:\batch\find.exe c:\SEQ -type f -iname *.sra > %temp%\SEQ_files_to_process.lst
for /f "delims=" %%i in (%temp%\SEQ_files_to_process.lst) do (fastq-dump --split-files --gzip %%i)


Share this post

Link to post
Share on other sites

Create an account or sign in to comment

You need to be a member in order to leave a comment

Create an account

Sign up for a new account in our community. It's easy!

Register a new account

Sign in

Already have an account? Sign in here.

Sign In Now
Sign in to follow this  
Followers 0

  • Recently Browsing   0 members

    No registered users viewing this page.