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Errors trying to use all files of a type

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# 8  
Old 09-16-2015
Thank you very much.

Are the two variables $pref and $prefix different? Thank you Smilie
# 9  
Old 09-17-2015
Quote:
Originally Posted by cmccabe
Thank you very much.

Are the two variables $pref and $prefix different? Thank you Smilie
There was nothing in this thread that set or referenced the shell variable pref until you asked this question. Without knowing how you set pref, there is no way that we can guess whether or not the shell variable expansion $pref will expand to the same string as the shell variable expansion $prefix.
# 10  
Old 09-17-2015
Here is my bash loop that works perfectly.

Code:
  for f in /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/*.bam ; do
      bname=`basename $f`
      pref=${bname%%.bam}
      samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${pref}_newheader.bam
 done

I also tried the below with no luck:

Code:
  for f in /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/*.bam ; do
      bname=`basename $f`
      prefix=${f%%.bam}
      samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${prefix}_newheader.bam
 done
  bash: /home/cmccabe/Desktop/NGS/pool_I_090215/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902_newheader.bam: No such file or directory
bash: /home/cmccabe/Desktop/NGS/pool_I_090215/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_015_rawlib_newheader.bam: No such file or directory
bash: /home/cmccabe/Desktop/NGS/pool_I_090215/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_016_150902_newheader.bam: No such file or directory

I am just curious why the second command was looking for the output in the directory. Thank you Smilie.
Last edited by cmccabe; 09-17-2015 at 11:09 AM.. Reason: edit format
# 11  
Old 09-17-2015
Quote:
Originally Posted by cmccabe
Here is my bash loop that works perfectly.

Code:
  for f in /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/*.bam ; do
      bname=`basename $f`
      pref=${bname%%.bam}
      samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${pref}_newheader.bam
 done

I also tried the below with no luck: [...]
bname=${f##*/} will always be faster than bname=`basename $f`

You are not working with the same variable. In pref you use bname as the base; in prefix, you are using the f variable and not bname.

Perhaps this demo will clarify:

Code:
[cmccabe]$ f="/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam"
[cmccabe]$ echo $f
/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902.bam
[cmccabe]$ bname=`basename $f`
[cmccabe]$ echo $bname
IonXpress_008_150902.bam
[fcmccabe]$ pref=${bname%%.bam}
[cmccabe]$ echo $pref
IonXpress_008_150902
[cmccabe]$ 
[cmccabe]$ prefix=${f%%.bam}
[cmccabe]$ echo $prefix
/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_008_150902
[cmccabe]$

I highlighted the difference
This User Gave Thanks to Aia For This Post:
cmccabe
# 12  
Old 09-17-2015
Thank you for clarifying and for the great demo Smilie
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