[Bioperl-l] Bioperl "align is not recognized as internal or external command"

[Fields, Christopher J]

It works on Mac (I recall it works on Linux as well).  The executable is named ‘clustalw2’, which can be symlinked to ‘clustalw’ if needed.  We could probably add support to deal with this...

chris

[cjfields at pyrimidine-laptop bioperl-run (master)]$ clustalw -help | head -n 4

 CLUSTAL 2.1 Multiple Sequence Alignments
[cjfields at pyrimidine-laptop bioperl-run (master)]$ prove -lrv t/Clustalw.t
t/Clustalw.t ..
1..45
ok 1 - use Bio::Tools::Run::Alignment::Clustalw;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::AlignIO;
ok 4 - use Bio::SeqIO;
ok 5 - use File::Spec;
ok 6 - Found input file
ok 7 - Found profile1 file
ok 8 - Found profile2 file
ok 9 - An object of class 'Bio::Tools::Run::Alignment::Clustalw' isa 'Bio::Tools::Run::Alignment::Clustalw'
ok 10 - program_dir returned correct default
ok 11 - error_string returned correct default
ok 12 - outfile_name returned correct default
ok 13 - bootstrap returned correct default
ok 14 - Correct exe default name
ok 15 - Supported program version 2.1
ok 16 - No error occured
ok 17 - outfile_name returned something
ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 19 - Correct number of seqs returned
ok 20 - Score
ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 22 - Correct number of seqs returned
ok 23 - Got correct sequence by position
ok 24 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree'
ok 25 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 26 - Correct number of seqs returned
ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 28 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree'
ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 30 - An object of class 'Bio::Tree::Tree' isa 'Bio::Tree::Tree'
ok 31 - footprinting worked
ok 32 - Got correct sequence by position
ok 33 - Got correct sequence by position
ok 34 - Set and got ktuple correctly
ok 35 - Set and got topdiags correctly
ok 36 - Set and got window correctly
ok 37 - Set and got pairgap correctly
ok 38 - Set and got fixedgap correctly
ok 39 - Set and got floatgap correctly
ok 40 - Set and got matrix correctly
ok 41 - Set and got type correctly
ok 42 - Set and got output correctly
ok 43 - Set and got outfile correctly
ok 44 - set and got quiet correctly
ok 45 - set and got bootstrap correctly
ok
All tests successful.
Files=1, Tests=45,  2 wallclock secs ( 0.03 usr  0.01 sys +  2.01 cusr  0.22 csys =  2.27 CPU)
Result: PASS

On May 15, 2014, at 6:57 AM, Paul Cantalupo <pcantalupo at gmail.com> wrote:

> Hi all,
> 
> I forgot to add bioperl list to my reply to Anil. This may help somebody
> else with the same problem. Can somebody chime in if this should be
> reported as a bug?
> 
> Thank you,
> 
> Paul
> 
> Paul Cantalupo
> University of Pittsburgh
> 
> 
> ---------- Forwarded message ----------
> From: Anil Kumar <anikng at gmail.com>
> Date: Wed, May 14, 2014 at 9:19 PM
> Subject: Re: [Bioperl-l] Bioperl "align is not recognized as internal or
> external command"
> To: Paul Cantalupo <pcantalupo at gmail.com>
> 
> 
> Hi Cantalupo,
> 
> As you mentioned, it was the problem with ClustalW version. When i
> re-installed older version of ClustalW 1.8, it worked...!!
> Thank you very much for your good suggestion.!!!
> 
> An Lee, Seoul,
> ROK
> 
> 
> On Thu, May 15, 2014 at 12:10 AM, Paul Cantalupo <pcantalupo at gmail.com>wrote:
> 
>> Hi,
>> 
>> I'm not sure if you are having the same issue, but check out:
>> http://www.perlmonks.org/?node_id=718819
>> 
>> Paul
>> 
>> 
>> 
>> Paul Cantalupo
>> University of Pittsburgh
>> 
>> 
>> On Thu, May 1, 2014 at 12:47 AM, <anikng at gmail.com> wrote:
>> 
>>> Hi Forum members,
>>> 
>>> My purpose is to do multiple sequence alignment using perl script and
>>> Bioperl mdules. For that I installed Bioperl  and Clusalw2 (2.1) in my
>>> Windows 7. When i tried to run a small code (attached below), it is
>>> showing
>>> some error
>>> as "align is not recognized as internal or external command etc etc.. A
>>> screen shot is attached.
>>> 
>>> I saw someone post similar error, but could not find any solution. So,
>>> kindly suggest me the solution.
>>> 
>>> 
>>> An Lee, Seoul,
>>> ROK
>>> 
>>> 
>>> 
>>> Code,
>>> 
>>> #!/usr/bin/perl
>>> use Bio::Seq;
>>> use Bio::Tools::Run::Alignment::Clustalw;
>>> use Bio::AlignIO;
>>> 
>>> BEGIN { $ENV{CLUSTALDIR} = 'C:/ClustalW2/clustalw2.exe'}
>>> 
>>> $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM');
>>> $ktuple = 3;
>>> $factory->ktuple($ktuple);  # change the parameter before executing
>>> 
>>> $in="1.fasta";
>>> $aln = $factory->align($in);
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>> 
>> 
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