10 Mar 2013 22:59
Re: sh: 1: Syntax error: "(" unexpected
Antony03 <antony.vincent.1 <at> ulaval.ca>
2013-03-10 21:59:51 GMT
2013-03-10 21:59:51 GMT
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 >> >> > > -- > View this message in context: > http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35155738.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l <at> lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l <at> lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- -- View this message in context: http://old.nabble.com/sh%3A-1%3A-Syntax-error%3A-%22%28%22-unexpected-tp35154292p35158468.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
RSS Feed