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Bash loop to result in one file

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Top Forums Shell Programming and Scripting Bash loop to result in one file
# 1  
Old 09-16-2015
Bash loop to result in one file
Is there a way to use a directory with multiple files (.bam) to create one new file? The below bash loop will create a new file (header.sam) for each of the bam files. However, I only need to use 1 of the bam file to make 1 header file. I attempted a code as well, but not sure if thats right.Thank you Smilie.

So in this example there are 3 .bam files and the loop with create a new header file for each. However only one header file is needed.

Code:
123.bam
456.bam
789.bam

header.sam

Code:
     for f in /home/cmccabe/Desktop/NGS/pool_I_090215/*.bam ; do
     bname=`basename $f`
     pref=${bname%%.bam}
     samtools view -H $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${pref}_header.sam
 done

Maybe:
Code:
     find f in /home/cmccabe/Desktop/NGS/pool_I_090215/*.bam ; do
     bname=`basename $f`
     samtools view -H $f > /home/cmccabe/Desktop/NGS/pool_I_090215/header.sam
 done

Last edited by cmccabe; 09-16-2015 at 03:45 PM.. Reason: fixed formatting
# 2  
Old 09-16-2015
Not sure I understand. If you want just one file - no matter which - why do run a loop and not one single command?
# 3  
Old 09-16-2015
A single command is what I am doing, but I am trying to make it so that the exact filename doesn't need to be used only the directory. Since the bam files change daily, it makes it a bit difficult to use. The directory is always the same. Thank you Smilie.

The individual command is:

Code:
samtools view -H IonXpress_009_150603.bam > header.sam

I am trying to do something like:

Code:
samtools view -H /home/cmccabe/Desktop/NGS/pool_I_090215/*.bam > header.sam

Thank you Smilie.
Last edited by cmccabe; 09-16-2015 at 04:08 PM.. Reason: added a couple lines
# 4  
Old 09-17-2015
So - how about samtools view -H $(ls /home/cmccabe/Desktop/NGS/pool_I_090215*.bam | head -1) > header.sam
This User Gave Thanks to RudiC For This Post:
cmccabe
# 5  
Old 09-17-2015
Code:
for f in /home/cmccabe/Desktop/NGS/pool_I_090215/*.bam ; do
     samtools view -H $f
done > entireloopfile

This User Gave Thanks to Corona688 For This Post:
cmccabe
# 6  
Old 09-18-2015
Thank you Smilie.
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