Paul Cantalupo | 15 May 13:57 2014
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Fwd: Bioperl "align is not recognized as internal or external command"

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
>>
>
>

Gmane