[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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