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Gmane
From: Smithies, Russell <Russell.Smithies <at> agresearch.co.nz>
Subject: Re: sh: 1: Syntax error: "(" unexpected
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Sunday 10th March 2013 20:30:36 UTC (over 3 years ago)
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: [email protected]
[mailto:[email protected]] On Behalf Of Antony03
Sent: Monday, 11 March 2013 2:17 a.m.
To: [email protected]
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:
[email protected]:~/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 
> 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
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

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