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Running a script over a series of files

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# 1  
Old 03-27-2013
Running a script over a series of files
Hi,

I want to run a script over a series of files with the names :

Sample_1.sorted.bam
Sample_2.sorted.bam
Sample_3.sorted.bam

How can I specify it in my script. Thanks a lot in advance.
# 2  
Old 03-27-2013
What have you tried so far?
# 3  
Old 03-27-2013
I think you're looking for this kind of code:
Code:
for file in *.bam; do
  echo $file
  # do something
  # do something else
done

Or more specific file spec:
Code:
for file in Sample_*.sorted.bam; do
  echo $file
  # do something
  # do something else
done

Hope this helps.
# 4  
Old 03-27-2013
By the way if you want to pass these file names as arguments to your script, use shell ENV variable $@
Code:
./your_script Sample_1.sorted.bam Sample_2.sorted.bam Sample_3.sorted.bam

"$@" is replaced with all command line argument.

Also note that white-space within an argument is preserved when enclosed in double quotes.
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