Jump to content
Strawberry Orange Banana Lime Leaf Slate Sky Blueberry Grape Watermelon Chocolate Marble
Strawberry Orange Banana Lime Leaf Slate Sky Blueberry Grape Watermelon Chocolate Marble

MSFN is made available via donations, subscriptions and advertising revenue. The use of ad-blocking software hurts the site. Please disable ad-blocking software or set an exception for MSFN. Alternatively, register and become a site sponsor/subscriber and ads will be disabled automatically. 



Sign in to follow this  
Adjuvant

Batch Command Help

Recommended Posts

Adjuvant    0

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.

Thanks!!!

Edited by Adjuvant

Share this post


Link to post
Share on other sites

allen2    1

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  

  • Recently Browsing   0 members

    No registered users viewing this page.

×