shell script for copying files with consecutive numbers

[JQL]

Hi all,

I have 170 fastq files from miSeq. They are named as 1_Sxx_L001…, 2_Sxx_L001…, 3_Sxx_L001… consecutively.

If I only need files from 1 to 120. How to quickly copy those files? I was thinking about using a for loop, but keep getting errors.

I can try this, but inefficient and error prone.
cp [1-9]_*.gz;
cp [1-9][0-9]_*.gz;
cp [1-9][0-1][0-9]_*.gz;
cp 120.*gz

thanks in advance.

example file names:

100_S122_L001_R1_001.fastq.gz 126_S145_L001_R2_001.fastq.gz 152_S168_L001_R1_001.fastq.gz 23_S71_L001_R2_001.fastq.gz 4_S36_L001_R1_001.fastq.gz 75_S34_L001_R2_001.fastq.gz
100_S122_L001_R2_001.fastq.gz 127_S155_L001_R1_001.fastq.gz 152_S168_L001_R2_001.fastq.gz 24_S82_L001_R1_001.fastq.gz 4_S36_L001_R2_001.fastq.gz 76_S45_L001_R1_001.fastq.gz

[GenoMax]

Where are you copying them from or to?

You can generate the numbers you need using a bash for loop like this easily

for i in `seq 1 120`; do echo $i; done

[JQL]

Those files belong to 3 projects. Lets say I want to copy the 120 files to the directory called project1.

for i in `seq 1 120`
do
cp "$1_*.fastq.gz" ~/project1/ ## it doesn't work.
done

thanks

Where are you copying them from or to?

You can generate the numbers you need using a bash for loop like this easily

for i in `seq 1 120`; do echo $i; done

[GenoMax]

That should be a $i (not 1).

for i in `seq 1 120`
do
cp $i\_*.fastq.gz ~/project1/
done

[JQL]

how come I copied all 170 files (since they are PE, so 340) over? Should be 240. Was it to due the "_"?

$ for i in `seq 1 120`; do cp $i_*fastq.gz ~/project1/; done

$ ls |wc -l
340

[GenoMax]

The _ should have been escaped. Corrected code above. Replace "echo" instead of "cp" to make sure all looks good first.

[JQL]

yes, it was the "_".

thanks!

$ ls | wc -l
240

[JQL]

what does underscore mean without escaped?

The _ should have been escaped. Corrected code above. Replace "echo" instead of "cp" to make sure all looks good first.

[GenoMax]

Run the following to see the difference

for i in `seq 1 120`
do
echo cp $i_*.fastq.gz ~/project1/
done

[JQL]

I ran it before. It copied all the *.gz files over (more than 2x120).
Interestingly, when I removed the copies in project1,
it copied again, removed, recopied.

any explanation?

Run the following to see the difference

for i in `seq 1 120`
do
echo cp $i_*.fastq.gz ~/project1/
done