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Errors trying to use all files of a type

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# 1  
Old 09-15-2015
Errors trying to use all files of a type
I am trying to create a code that will use all the bam files stored on a separate drive (/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215), run them in a program that I have changed the directory to, and the output gets re-directed to (/home/cmccabe/Desktop/NGS/pool_I_090215). I have tried the script two ways getting two different errors and cant seem to fix it. the bold in the second error is the output so why is it looking for those files Thank you Smilie.

Code:
cmccabe@HPZ640:~$ cd "/home/cmccabe/Desktop/NGS"
cmccabe@HPZ640:~/Desktop/NGS$ for f in /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/*.bam do 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: syntax error near unexpected token `|'


cmccabe@HPZ640:~/Desktop/NGS$ for f in /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/*.bam
> do
> 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

# 2  
Old 09-15-2015
You are just removing the '.bam', you are not removing the long pathname.

Try FILE=$(basename "$FILE") to remove the path.
# 3  
Old 09-15-2015
The below code runs but no output is created. Thank you Smilie.

Code:
cmccabe@HPZ640:~/Desktop/NGS$ FILE=$(basename "$FILE")
cmccabe@HPZ640:~/Desktop/NGS$ for f
> do
> prefix=${f%%.bam}
> samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${prefix}_newheader.bam
> done

tried this as well:
Code:
 cmccabe@HPZ640:~/Desktop/NGS$ for f in /media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/*.bam
> FILE=$(basename "$FILE")
bash: syntax error near unexpected token `FILE=$(basename "$FILE")'
cmccabe@HPZ640:~/Desktop/NGS$ do
bash: syntax error near unexpected token `do'
cmccabe@HPZ640:~/Desktop/NGS$ prefix=${f%%.bam}
cmccabe@HPZ640:~/Desktop/NGS$ samtools view -H $f | sed '/^@PG/d' | samtools reheader - $f > /home/cmccabe/Desktop/NGS/pool_I_090215/${prefix}_newheader.bam
bash: /home/cmccabe/Desktop/NGS/pool_I_090215//media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215/IonXpress_016_150902_newheader.bam: No such file or directory

Last edited by cmccabe; 09-15-2015 at 06:15 PM.. Reason: added another code
# 4  
Old 09-15-2015
Tried what? What exactly did you do? The code is scrambled by all the errors.

Why are you using FILE when your variable is named f?
This User Gave Thanks to Corona688 For This Post:
cmccabe
# 5  
Old 09-15-2015
I guess im not sure how to use basename. Thank you Smilie.
# 6  
Old 09-15-2015
Quote:
Originally Posted by cmccabe
I guess im not sure how to use basename. Thank you Smilie.
The same technique as prefix=${f%%.bam} can be used to obtain the name of the file without the path
Code:
base_name=${f##*/}

This User Gave Thanks to Aia For This Post:
cmccabe
# 7  
Old 09-16-2015
And chained
Code:
basename=${f##*/}
prefix=${basename%%.bam}

This User Gave Thanks to MadeInGermany For This Post:
cmccabe
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