[Bioperl-l] sh: 1: Syntax error: "(" unexpected

[Smithies, Russell]

I suspect that there's several versions of water and the parameters have changed.
This is the version I'm using and I can reproduce the errors:

intrepid$ water -h
Smith-Waterman local alignment of sequences
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -gapopen            float      [10.0 for any sequence] The gap open penalty
                                  is the score taken away when a gap is
                                  created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value assumes you are using the EBLOSUM62
                                  matrix for protein sequences, and the
                                  EDNAFULL matrix for nucleotide sequences.
                                  (Number from 0.000 to 100.000)
   -gapextend          float      [0.5 for any sequence] The gap extension
                                  penalty is added to the standard gap penalty
                                  for each base or residue in the gap. This
                                  is how long gaps are penalized. Usually you
                                  will expect a few long gaps rather than many
                                  short gaps, so the gap extension penalty
                                  should be lower than the gap penalty. An
                                  exception is where one or both sequences are
                                  single reads with possible sequencing
                                  errors in which case you would expect many
                                  single base gaps. You can get this result by
                                  setting the gap open penalty to zero (or
                                  very low) and using the gap extension
                                  penalty to control gap scoring. (Number from
                                  0.000 to 10.000)
  [-outfile]           align      [*.water] Output alignment file name
                                  (default -aformat srspair)

   Additional (Optional) qualifiers:
   -datafile           matrixf    [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.

   Advanced (Unprompted) qualifiers:
   -[no]brief          boolean    [Y] Brief identity and similarity

   General qualifiers:
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Antony03
Sent: Sunday, 10 March 2013 3:59 p.m.
To: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] sh: 1: Syntax error: "(" unexpected


Hi! Yes I'm sure, my script is exactly what I posted here. And I run it like
this:
anvin26 at anvin26:~/Bureau/emboss$ perl water.pl
sh: 1: Syntax error: "(" unexpected
So, I think there is no ambiguity (I run it like a perl script) and this why I don't understand why the script is run like a bash script!


Leon Timmermans-2 wrote:
> 
> On Sat, Mar 9, 2013 at 4:56 AM, Antony03 <antony.vincent.1 at ulaval.ca>
> wrote:
>> 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
> 
> The error suggests the script is interpreted by the shell instead of 
> perl. Are you sure the hashbang (#!) is the absolute first thing in 
> the file. No whitespace or BOM character in the front?
> 
> Leon
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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