[Bioperl-l] sh: 1: Syntax error: "(" unexpected
Liam Elbourne
liam.elbourne at mq.edu.au
Sat Mar 9 11:39:44 UTC 2013
Hi Antony,
How are you trying to run this? Are you by any change trying to run it as a shell script? I get no syntax or runtime errors when I run it from the command line, ie saved as a file called say "run_emboss.pl", then typing "./run_emboss.pl" at the prompt.
Regards,
Liam.
On 09/03/2013, at 2:56 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>
> Hi!
>
> I'm trying to use emboss program (water or needle) with a bioperl script. I
> got this error when I try the script: sh: 1: Syntax error: "(" unexpected
>
> Here is the script:
>
> #!/usr/bin/perl
>
> # get an EMBOSS factory
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
> use Bio::SeqIO;
> $f = Bio::Factory::EMBOSS -> new();
> # get an EMBOSS application object from the factory
> $water = $f->program('water');
> $inputfilename = "krt1.fasta";
> $seq_to_test = Bio::SeqIO->new(-file => $inputfilename ,
> '-format' => 'fasta');
>
> $inputfilename2 = "krt2.fasta";
> @seqs_to_check = Bio::SeqIO->new(-file => $inputfilename2 ,
> '-format' => 'fasta');
> # here is an example of running the application -
> # water can compare 1 sequence against 1 or more sequences
> # in a database using Smith-Waterman
> #this would be a list of seqs to compare
> # (could be just 1)
> my $wateroutfile = 'out.water';
> $water->run({-sequences => $seq_to_test,
> -seqall => \@seqs_to_check,
> -gapopen => '10.0',
> -gapextend => '0.5',
> -outfile => $wateroutfile});
> # now you might want to get the alignment
>
> my $alnin = Bio::AlignIO->new(-format => 'emboss',
> -file => $wateroutfile);
>
> while ( my $aln = $alnin->next_aln ) {
> # process the alignment -- these will be Bio::SimpleAlign objects
> }
>
> Have you an idea of what can do this error?
>
> Thanks!
> --
> View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35154292.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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