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using command line version meme suite to output multiple files

Hi everyone,

i have a large folder contains thousands of files which all have to be process by meme

the command i used is ' meme FILENAME -mod dna', however the results were overwritten itself everytime , i know i can set the output directory using -o DIRECTORY, but how can i do this in an automatic fashion for all the files may be using a for loop in bash and output the files in different directories??

many thanks

meme suite
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updated by GenoMax GenoMax • written by kws15 • kws15

1 answer 

for i in $(ls FILENAME); do mkdir $i\_dir; meme $i -mod dna -o $i\_dir; done

This is just an outline of what can be done. You would want to parse the filename and take parts of it to make the actual output directory name. See @Ram's answer in this bash loop for alignment RNA-seq data for an idea about how to parse file names.

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written by GenoMax GenoMax

thank you very much! that works

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written by kws15 • kws15

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