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

Fields, Christopher J cjfields at illinois.edu
Mon Mar 11 20:57:59 UTC 2013


I think the EMBOSS code checks the ACD file for whatever version of EMBOSS is installed, parses the parameters out of that, and uses those for input.  I don't remember if it accepts a Bio::Seq as input (I don't recall it doing so), but if it does then we should file that as a bug.

chris

On Mar 11, 2013, at 1:09 PM, "Smithies, Russell" <Russell.Smithies at agresearch.co.nz> wrote:

> 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
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>> 
>> 
> 
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