Renaming multiples files with a bash loop
-
17-04-2021 - |
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 $NEWNAME
done
But it doesn't work. Can you tell me why, or give another quick solution?
Thanks!
La solution
Several mistakes here:
NEWNAME =
should be without space. Here bash is looking for a command namedNEWNAME
and that fails.- you parse the output of ls. this is bad if you had files with spaces. Bash can build itself a list of files with the glob operator
*
. - You don't escape
"$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
.
Autres conseils
for f in chr*.fasta; do mv "$f" "${f/%.fasta/.fa}"; done
If you have the rename
command, you can do:
rename .fasta .fa chr*.fasta
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