Adjuvant Posted October 29, 2012 Share Posted October 29, 2012 (edited) 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*.sraI 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.sraI 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 *.sraor fastq-dump --split-files --gzip SRP*\SRS*\SRX*\SRR*\SRA*.srabut it doesn't appear fastq-dump supports *.sraI am inept at batching files. I just need simple code to run fastq-dump --split-files --gzip SRXXXXX1.sraand 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 October 29, 2012 by Adjuvant Link to comment Share on other sites More sharing options...
allen2 Posted October 30, 2012 Share Posted October 30, 2012 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.lstfor /f "delims=" %%i in (%temp%\SEQ_files_to_process.lst) do (fastq-dump --split-files --gzip %%i) Link to comment Share on other sites More sharing options...
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