Create new file with old filename using bash

Question

I have a script that I need to run on every file in a folder. The script creates a new file with the same name as the original file in a new folder.

So the folder contains files with names like:

SLX-8691.ART12.seq
SLX-8690.ART12.seq
SLX-8692.ART12.seq
SLX-8693.ART12.seq

The script I want to run on every file isexample is as follows:

$ ./unique_seq_counts.rb ./qualitymask/SLX-8691.ART12.seq > ./uniquecounts/SLX-8691.ART12.counts.txt

So that SLX-8691.ART12.seq is replaced by each file name.

Is there a way of looping through a replacing each filename automatically?

Thanks

Yes, you use variables. You can use reference them when renaming as if they were strings. They'll be expanded. There are multiple examples of similar stuff here on SO and on superuser. — keyser
– keyser, Commented Aug 2, 2014 at 12:21

konsolebox · Accepted Answer · 2014-08-02 13:05:21Z

1

Using a loop:

for F in ./qualitymask/*.seq; do
   T=${F##*/}  ## Removes directory part. Same as $(basename "$F")
   T=${T%.seq}.counts.txt  ## Removes .seq and adds .counts.txt
   ./unique_seq_counts.rb "$F" > "./uniquecounts/$T"
done

See: Parameter Expansion and Filename Expansion.

answered Aug 2, 2014 at 13:05

konsolebox

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