Splitting multiple files in a folder


 
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# 1  
Splitting multiple files in a folder

Hello,

I am new to UNIX etc and am trying to split a large number of files, all with the extension .fas in the same folder, into smaller files wherever a string of 5ns occurs.

So this file:

>File1.fas
nnnnnaaaaaattgattttctcagtatcgacgaatatggcgcagaaagttgaataa
nnnnnaatcaacatagaaatacaataaaaaaattttatatttactattttaataatattt


Would be split into two files, one called

File1.fas01 and containing

nnnnnaaaaaattgattttctcagtatcgacgaatatggcgcagaaagttgaataa


And the second called


File1.fas02 and containing
nnnnnaatcaacatagaaatacaataaaaaaattttatatttactattttaataatattt


This perl script below works well but, I don't know how to apply to all 201 files in the same folder separately.

perl -n -e '/nnnnn/ and open FH, ">$ARGV".$n++; print FH;' *.fas

I would appreciate any pointers towards how to process lots of files in one go with the same script.

Thanks very much!
# 2  
I think you really want the csplit command:

Code:
cd /path/to/files
for fname in *.fas
do
   csplit $fname /nnnnn/
done

There are options for setting the names of your output files, play around with those - see the csplit man page.
This User Gave Thanks to jim mcnamara For This Post:
 

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