Renaming multiples files with a bash loop

Question

I need to rename 45 files, and I don't want to do it one by one. These are the file names:

chr10.fasta         chr13_random.fasta  chr17.fasta         chr1.fasta          chr22_random.fasta  chr4_random.fasta  chr7_random.fasta  chrX.fasta
chr10_random.fasta  chr14.fasta         chr17_random.fasta  chr1_random.fasta   chr2.fasta          chr5.fasta         chr8.fasta         chrX_random.fasta
chr11.fasta         chr15.fasta         chr18.fasta         chr20.fasta         chr2_random.fasta   chr5_random.fasta  chr8_random.fasta  chrY.fasta
chr11_random.fasta  chr15_random.fasta  chr18_random.fasta  chr21.fasta         chr3.fasta          chr6.fasta         chr9.fasta         
chr12.fasta         chr16.fasta         chr19.fasta         chr21_random.fasta  chr3_random.fasta   chr6_random.fasta  chr9_random.fasta
chr13.fasta         chr16_random.fasta  chr19_random.fasta  chr22.fasta         chr4.fasta          chr7.fasta         chrM.fasta

I need to change the extension ".fasta" to ".fa". I'm trying to write a bash script to do it:

for i in $(ls chr*)

do

NEWNAME = `echo $i | sed 's/sta//g'`

mv $i $NEWNAME

done

But it doesn't work. Can you tell me why, or give another quick solution?

Thanks!

Benoit · Accepted Answer · 2012-01-18 08:43:58Z

45

Several mistakes here:

NEWNAME = should be without space. Here bash is looking for a command named NEWNAME and that fails.
you parse the output of ls. this is bad if you had files with spaces. Bash can build itself a list of files with the glob operator *.
You don't escape "$i" and "$NEWNAME". If any of them contains a space it makes two arguments for mv.
If a file name begins with a dash mv will believe it is a switch. Use -- to stop argument processing.

Try:

for i in chr*
do
  mv -- "$i" "${i/%.fasta/.fa}"
done

or

for i in chr*
do
  NEWNAME="${i/%.fasta/.fa}"
  mv -- "$i" "$NEWNAME"
done

The "%{var/%pat/replacement}" looks for pat only at the end of the variable and replaces it with replacement.

edited Jan 18, 2012 at 8:43

answered Jan 17, 2012 at 17:41

Benoit

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11 Comments

Benoit Over a year ago

@Chris Dodd: taking good habits is though so useful afterwards.

Chris Dodd Over a year ago

One man's virtue is another man's vice -- Encouraging the use of spaces in filenames (or files that begin with -) is not a good thing.

Benoit Over a year ago

Why is it not a good thing? Because programmers don't always correctly handle them? Ask the end users of computer workstations to remove all spaces, dashes, and non-alphanumeric characters from their filenames and spot their reaction :) As programmers it is our job to adapt to the possibilities of the systems we work on. As for files that begin with - why couldn't I name a file starting with a negative number for instance?

Josh Over a year ago

What does mv -- do? I've found it elsewhere but can't figure out what it does.

Benoit Over a year ago

@Josh -- signifies end of option parsing. Therefore, if you have a file named -i for example, mv -- -i … will work because -i will not be interpreted as a switch.

|

Chris Dodd · Accepted Answer · 2012-01-17 19:19:44Z

14

for f in chr*.fasta; do mv "$f" "${f/%.fasta/.fa}"; done

edited Jan 17, 2012 at 19:19

answered Jan 17, 2012 at 17:42

Chris Dodd

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5 Comments

c00kiemon5ter Over a year ago

althought this would work with the given data, what about spaces in files, or files that contain .fasta in their filename and not only as their extension ? many things can go wrong here

c00kiemon5ter Over a year ago

fixed use of /% before I even got to post the above comment ;)

Chris Dodd Over a year ago

Ok, I added the quotes even though they almost certainly aren't needed, given the OP's example. There also aren't likely any spurious periods in the names.

Benoit Over a year ago

@Chris Dodd: so, now your answer is very similar to mine :) And always quoting is taking good habits. I used to use them lazily and one day came the disaster.

jordanm Over a year ago

Removed downvote since files with spaces issue is fixed. Always use best practices when teaching others!

dogbane · Accepted Answer · 2012-01-17 17:45:48Z

7

If you have the rename command, you can do:

rename .fasta .fa chr*.fasta

answered Jan 17, 2012 at 17:45

dogbane

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