Antony03 | 10 Mar 22:59 2013
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Re: sh: 1: Syntax error: "(" unexpected


That's works! Thanks a lot!

Smithies, Russell wrote:
> 
> 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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Gmane