[Bioperl-l] sh: 1: Syntax error: "(" unexpected
Smithies, Russell
Russell.Smithies at agresearch.co.nz
Sun Mar 10 20:30:36 UTC 2013
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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