execute VelvetOptimiser from perl script

[bpich]

Hello,
I am trying to run velvetoptimiser using the perl system command my script is like this:
my @velvetcmd;
my $velvetpath="/opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl";
push @velvetcmd,$velvetpath;
my $velvetarg=" -v -s 27 -e 31 -f '-fastq -shortPaired $reportdir/velvet/$nameseq.shuffled.fastq.gz' -p $velvetdir/$nameseq\_assembly";
push @velvetcmd,$velvetarg;
my $velvetcmdstr= join (" ",@velvetcmd);
system ('perl',$velvetpath,$velvetcmdstr) or die ;

I have the error message from :
You must supply the velveth parameter line in quotes. eg -f '-short .....'
Usage: /opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl [options] -f 'velveth input line'

Thanks for helping
b

[GenoMax]

Have you tried "escaping" single quotes (e.g. http://stackoverflow.com/questions/5...single-quote)?

[bpich]

yes, it returns the same error!

[GenoMax]

Any reason why you are doing this via Perl and not directly on the command line? BTW you appear to be missing velveth in the -f part of your command line.

[bpich]

I' d like to call velvetoptimiser as part of a perl script which loop through list of sequences.
what do you mean missing velveth?
When I run the same string on command line it works! Should I change the argument I pass through system?

[mastal]

I don't think you have to specify velveth.

This is from the VelvetOptimiser manual:

VelvetOptimiser.pl [options] -f 'velveth input line'

and an example:

% VelvetOptimiser.pl -s 27 -e 31 -f '-short -fastq s_1_sequence.txt'

https://raw.githubusercontent.com/Victorian-Bioinformatics-Consortium/VelvetOptimiser/master/README

[GenoMax]

Usage: /opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl [options] -f 'velveth input line'.

Above message from your first post threw me off but looking at the VelvetOptimiser.pl help that is not needed. Trying to understand how you are constructing the command line.

[mastal]

@bpich

I'm not that familiar with the system() command,

but it seems that you are givng the path twice, once in $velvetpath, and again in $velvetcmdstr.

what happens if you try:
system ('perl',$velvetpath,$velvetarg) or die ;

[GenoMax]

See if this modification to the two lines works with rest of your code (with @mastal's suggestion).

my @velvetcmd;
my $velvetpath="/opt/software/velvet/1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOptimiser.pl";
push @velvetcmd,$velvetpath;
my $velvetarg=" -v -s 27 -e 31 -f '-fastq -shortPaired $reportdir/velvet/$nameseq.shuffled.fastq.gz' -p $velvetdir/$nameseq\_assembly";
push @velvetcmd,$velvetarg;
my $velvetcmdstr= join (" ",@velvetcmd);
system ("perl ",$velvetpath,$velvetarg) or die ;

[bpich]

Thanks! modifications work well
b