Running stampy in bash script

[grafab]

Hi folks,

I try to run stampy from a bash script. My problem is more a Unix/bash issue, but some of you may have a working script already, so I hope you can help me.
My script:
...
q10="-q10"
bwa_opt=$q10" "$bwa_ref

command=$stampy' -g '$ref_genome' -h '$ref_genome' -o '$out' --bwa='$bwa' --bwaoptions="'$bwa_opt'" -M '$seq1' '$seq2

echo $command
$command

Output:
./stampy-1.0.17/stampy.py -g hg19 -h hg19 -o out.sam --bwa=./bwa-0.5.7/bwa --bwaoptions="-q10 ~/reference_genome/hg19.fa" -M sequ1.fastq sequ2.fastq
Nothing to do, with unused arguments on command line
First unused argument: '~/reference_genome/hg19.fa"'

The $command looks correct to me from the echo output, but it does not work in the script. When I copy the echo output and paste it to the command line, it does work. "Bash" makes a difference between echo $command and running $command. I could not figure out what is different. Maybe it is something about the quotes of --bwaoptions.

Thanks,
grafab

[Alex Renwick]

try this:

q10="-q10"
bwa_opt="$q10 $bwa_ref"
command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions='$bwa_opt' -M $seq1 $seq2"

[grafab]

Thank you for your quick reply!
Unfortunately it does not solve my problem.

Output with your code:

./stampy-1.0.17/stampy.py -g hg19 -h hg19 -o out.sam --bwa=./bwa-0.5.7/bwa --bwaoptions='-q10 ~reference_genome/hg19.fa' -M seq1.fastq seq2.fastq
Nothing to do, with unused arguments on command line
First unused argument: '/home/ben4571/tmp/reference_genome/hg19.fa''
0

(The last quotes are two single ones, not one double quote.)

I copied the command from the output and pasted it to the command line, as I did with my output before. Again, this way works very well. But it fails from within the script.

Any suggestions?

I use GNU bash, Version 4.2.10(1)-release (x86_64-suse-linux-gnu).

[grafab]

Now I used the "-v 3" option in the stampy call and got the following line in the output:

...
stampy: Starting Stampy with the following options:
...
bwaoptions="-q10
...

So apparently the stampy.py script has problems, parsing the arguments.
I just dont understand why it works from the command line...

[colindaven]

Perhaps use a very simple Perl script instead ?

I use generic scripts a lot to run aligners, taking arguments from the command line and running the aligner that way. It's very good for sharing to other users.

[grafab]

Perhaps use a very simple Perl script instead ?

I use generic scripts a lot to run aligners, taking arguments from the command line and running the aligner that way. It's very good for sharing to other users.

That works, thank you!
But I still would like to know, why the bash script is not working...

[Alex Renwick]

Thank you for your quick reply!
Unfortunately it does not solve my problem.

Output with your code:

./stampy-1.0.17/stampy.py -g hg19 -h hg19 -o out.sam --bwa=./bwa-0.5.7/bwa --bwaoptions='-q10 ~reference_genome/hg19.fa' -M seq1.fastq seq2.fastq
Nothing to do, with unused arguments on command line
First unused argument: '/home/ben4571/tmp/reference_genome/hg19.fa''
0

(The last quotes are two single ones, not one double quote.)

I copied the command from the output and pasted it to the command line, as I did with my output before. Again, this way works very well. But it fails from within the script.

Any suggestions?

I use GNU bash, Version 4.2.10(1)-release (x86_64-suse-linux-gnu).

The issue is how white space is being parsed by bash. The script does it's own parsing, then parsing happens again when the command is executed. It sometimes takes some trial and error before I get it right.
Here are some things I would try:

command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions=\"$q10 $bwa_ref\" -M $seq1 $seq2"
command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions=$q10\ $bwa_ref -M $seq1 $seq2"
command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions=\"$q10\ $bwa_ref\" -M $seq1 $seq2"
command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions=$q10\\\ $bwa_ref -M $seq1 $seq2"

[grafab]

Thank you all, for helping me!

I finally got it working. Thanks to the hint that the whitespace might be the problem, I found this HOW-TO. The solution is the eval command.

...
command="$stampy -g $ref_genome -h $ref_genome -o $out --bwa=$bwa --bwaoptions=\"$q10 $bwa_ref\" -M $seq1 $seq2"
eval $command