Francisco J. Ossandón | 15 May 18:27 2014
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Re: Bioperl "align is not recognized as internal or external command"

A little off topic question...

I also replied to Anil and the reply went to 'bioperl-l <at> googlegroups.com'
too (pointed out the problem with the CLUSTALDIR containing a file path). I
see my reply there
(https://groups.google.com/forum/#!topic/bioperl-l/36b6NDRD_6o) but not in
the bioperl-l mailing list archive
(http://lists.open-bio.org/pipermail/bioperl-l/2014-May/date.html). I
thought that the Google group reply would also be forwarded to the mailing
list, but it does not seem the case. Should I always add the copy to the
mailing list??

Now on topic with clustalw2. Taking the 'version' subroutine approach as
example (my $string = `$prog -- 2>&1` ;), for setting "our $PROGRAM_NAME"
value maybe "$PROGRAM_DIR /clustalw2" execution could be tested, and if it
fails test for "$PROGRAM_DIR /clustalw" execution and if that fails then
abort...

By the way, I went to Clustalw2 page
(http://www.ebi.ac.uk/Tools/msa/clustalw2/) and found a "Note: ClustalW2 is
no longer being maintained. Please consider using the new version instead:
Clustal Omega"! This means that now, besides 'clustalw2'
(http://www.clustal.org/clustal2/), there is a new version
(http://www.clustal.org/omega/) that also have a new executable name
'clustalo' (no idea if the arguments, inputs and outputs remains the same
than previous versions)... If clustalo can pass the same tests, then it
would have to be included as a valid executable name option.

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces <at> lists.open-bio.org
[mailto:bioperl-l-bounces <at> lists.open-bio.org] En nombre de Fields,
Christopher J
Enviado el: jueves, 15 de mayo de 2014 9:33
Para: Paul Cantalupo
CC: BioPerl List; Anil Kumar
Asunto: Re: [Bioperl-l] Bioperl "align is not recognized as internal or
external command"

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
>>> 
>> 
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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