[Bioperl-l] sh: 1: Syntax error: "(" unexpected
Antony03
antony.vincent.1 at ulaval.ca
Sun Mar 10 17:59:51 EDT 2013
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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