Smithies, Russell | 10 Mar 21:30 2013
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Re: sh: 1: Syntax error: "(" unexpected

I'll get in first and say it's best to 'use strict', and 'use warnings'  ;-)

Perhaps some of the params to water have changed? It looks like it wants filenames, not objects.
I get the same errors with your code - which I think is coming from water.

If I do this it seems to work OK:
---------------------------------------
#!/usr/bin/perl

# get an EMBOSS factory
use Bio::Factory::EMBOSS;
use Bio::AlignIO;
use Bio::SeqIO;

use strict;
use warnings;

my $f = Bio::Factory::EMBOSS -> new();
# get an EMBOSS application  object from the factory
my $water = $f->program('water');
my $wateroutfile = 'out.water';
$water->run({  -verbose => 1,
               -asequence => 'krt1.fasta',
               -bsequence => 'krt2.fasta',
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => 'out.water'});
------------------------------------------------

illustrious$ cat out.water
########################################
# Program: water
# Rundate: Mon 11 Mar 2013 09:29:36
# Commandline: water
#    -gapopen 10.0
#    -gapextend 0.5
#    -outfile out.water
#    -asequence krt1.fasta
#    -verbose 1
#    -bsequence krt2.fasta
#    -auto
# Align_format: srspair
# Report_file: out.water
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: K2C1_HUMAN
# 2: K22E_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     436/667 (65.4%)
# Similarity:   499/667 (74.8%)
# Gaps:          78/667 (11.7%)
# Score: 2023.5
#
#
#=======================================

K2C1_HUMAN         1 MSRQFSSRSGYRSGG-----GFSSGSAGIINYQRRTTSSSTRRSGGGGGR     45
                     ||.|.|.:|..|.||     |||||||.:....||:|||
K22E_HUMAN         1 MSCQISCKSRGRGGGGGGFRGFSSGSAVVSGGSRRSTSS-----------     39

K2C1_HUMAN        46 FSSC----GGGGGSFGAGGGFGSRSLVNLGGSKSISISVARGGGRGSGFG     91
                      .||    |||||.|| ||||||||||.|||:|||||||| |||.|.|..
K22E_HUMAN        40 -FSCLSRHGGGGGGFG-GGGFGSRSLVGLGGTKSISISVA-GGGGGFGAA     86

K2C1_HUMAN        92 GGYG--GGGFGGG-------GFGGGGFGGGGIGGGGFGGFGSGG--GGFG    130
                     ||:|  |||||||       ||.||||||||.|||.|||||..|  ||.|
K22E_HUMAN        87 GGFGGRGGGFGGGSSFGGGSGFSGGGFGGGGFGGGRFGGFGGPGGVGGLG    136

K2C1_HUMAN       131 G-GGFGGGGYGGGYGPVCPPGGIQEVTINQSLLQPLNVEIDPEIQKVKSR    179
                     | ||||.|||         ||||.||::||||||||||::|||||.||::
K22E_HUMAN       137 GPGGFGPGGY---------PGGIHEVSVNQSLLQPLNVKVDPEIQNVKAQ    177

K2C1_HUMAN       180 EREQIKSLNNQFASFIDKVRFLEQQNQVLQTKWELLQQVDTSTRTHNLEP    229
                     ||||||:|||:|||||||||||||||||||||||||||::..||..||||
K22E_HUMAN       178 EREQIKTLNNKFASFIDKVRFLEQQNQVLQTKWELLQQMNVGTRPINLEP    227

K2C1_HUMAN       230 YFESFINNLRRRVDQLKSDQSRLDSELKNMQDMVEDYRNKYEDEINKRTN    279
                     .|:.:|::|:|.:|.|.::::..:|||.||||:||||:.||||||||||.
K22E_HUMAN       228 IFQGYIDSLKRYLDGLTAERTSQNSELNNMQDLVEDYKKKYEDEINKRTA    277

K2C1_HUMAN       280 AENEFVTIKKDVDGAYMTKVDLQAKLDNLQQEIDFLTALYQAELSQMQTQ    329
                     |||:|||:|||||.|||.||:||:|:|.|.|||:||..||.||:||:...
K22E_HUMAN       278 AENDFVTLKKDVDNAYMIKVELQSKVDLLNQEIEFLKVLYDAEISQIHQS    327

K2C1_HUMAN       330 ISETNVILSMDNNRSLDLDSIIAEVKAQYEDIAQKSKAEAESLYQSKYEE    379
                     :::|||||||||:|:|||||||||||||||:|||:||.|||:||.|||||
K22E_HUMAN       328 VTDTNVILSMDNSRNLDLDSIIAEVKAQYEEIAQRSKEEAEALYHSKYEE    377

K2C1_HUMAN       380 LQITAGRHGDSVRNSKIEISELNRVIQRLRSEIDNVKKQISNLQQSISDA    429
                     ||:|.||||||::..||||||||||||||:.||.:||||..|:|.:|:||
K22E_HUMAN       378 LQVTVGRHGDSLKEIKIEISELNRVIQRLQGEIAHVKKQCKNVQDAIADA    427

K2C1_HUMAN       430 EQRGENALKDAKNKLNDLEDALQQAKEDLARLLRDYQELMNTKLALDLEI    479
                     |||||:|||||:|||||||:|||||||||||||||||||||.|||||:||
K22E_HUMAN       428 EQRGEHALKDARNKLNDLEEALQQAKEDLARLLRDYQELMNVKLALDVEI    477

K2C1_HUMAN       480 ATYRTLLEGEESRMSGECAPNVSVSVSTSHTTISG--------GGSRGGG    521
                     ||||.||||||.||||:.:.||:|||::|  |||.        |||.|.|
K22E_HUMAN       478 ATYRKLLEGEECRMSGDLSSNVTVSVTSS--TISSNVASKAAFGGSGGRG    525

K2C1_HUMAN       522 ---GGGYGSGGSSYGSGGGSYGSGGGGGGGRGSYGSGGSSYGSGGGSYGS    568
                        ||||.||.|||||||...||.||.||| ||.        |||| |||
K22E_HUMAN       526 SSSGGGYSSGSSSYGSGGRQSGSRGGSGGG-GSI--------SGGG-YGS    565

K2C1_HUMAN       569 GGGGGGHGSYGSGSSSGGYRGGS-GGGGGGSSGGR-GSGGGSSGGSIGGR    616
                     |||.||.  ||||   ||.:||| .|||.||.||: .|||||.|||..|.
K22E_HUMAN       566 GGGSGGR--YGSG---GGSKGGSISGGGYGSGGGKHSSGGGSRGGSSSGG    610

K2C1_HUMAN       617 GSSSGGVKSSGGSSSVK    633
                     |..|||    |||||||
K22E_HUMAN       611 GYGSGG----GGSSSVK    623

#---------------------------------------
#---------------------------------------

--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: Monday, 11 March 2013 2:17 a.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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