funziona sulla riga di comando ma non in uno script di shell

Question

Ho questa riga

samtools view -h file | awk '$3=="chr$a" || /^@/' | samtools view -S - -b -o output

.

Il trattino tra -s e il -b dovrebbe indicare al programma che è da STDIN.Posso eseguirlo da uno script perl sulla riga di comando, ma non appena provo a spostarlo in uno script di shell, crea solo il file senza emettere dati.Qualsiasi idea sarebbe molto apprezzata.

Answer 1

In a shell script the $a inside single quotes will not be expanded:

for a in {1..22} do 
  samtools view -h AD3.sorted.bam | awk '$3=="chr$a" || /^@/' | samtools view -S - -b -o chr$a.bam 
done 

Answer 2

If you haven't already, have a look at the samtools FAQ. This has examples for doing similar things to what you want to do with your pipeline.

Its been a while since I used samtools, but I would've written your command like this:

samtools view -h file | awk '$3=="chr$a" || /^@/' | samtools view -S -b - > output.bam

Also you mentioned you had moved the command to a shell script. Is the shell script doing anything else? If it still doesn't work, I would post that for us to look at.