bash shell question

[JQL]

I tried to do a simple task in batch--unzipping many gz files. I have many .gz files, but how come it only unzipped one file then finished? Anything wrong with my script? thanks. John


## unzip fastq.gz
for i in *.fastq.gz
do
#echo $i
zcat "$i" > "${i%.*}"
done

[azneto]

have you tried 'gunzip *.fastq.gz' ?

[JQL]

gunzip *.fastq.gz will delete original gz files. i want to keep original files.

Originally Posted by azneto

have you tried 'gunzip *.fastq.gz' ?

[azneto]

for i in `ls *.fastq.gz`; do gunzip -c $i > $i.fastq; done

[JQL]

I tried
for i in `ls *.fastq.gz`; do gunzip -c $i > ${i%.gz}; done

still only unzipped just first file then finished. no error. very strange.

Originally Posted by azneto

for i in `ls *.fastq.gz`; do gunzip -c $i > $i.fastq; done

[azneto]

I tested your version of the command and it worked fine. It could be something related to permissions.

[JQL]

thanks. I thought it might be related to something internal. will find out.

Originally Posted by azneto

I tested your version of the command and it worked fine. It could be something related to permissions.

[Richard Finney]

for i in $(ls *.gz); do sn=`echo $i | sed 's/\.gz$//'`; zcat $i > $sn; done;

[JQL]

another nice way to do it.

I really think something is going on with my server. It still finished after doing one file. I will ask my admin tomorrow. Will let you know.

By any chance did this happen to any one of you here?

Originally Posted by Richard Finney

for i in $(ls *.gz); do sn=`echo $i | sed 's/\.gz$//'`; zcat $i > $sn; done;