[Jalview-discuss] problem with fasta files

[Judith Cohn]

p.s. I have a similar problem with a clean install of the latest  
version of Java 2.4 on Linux.  It works similar to my colleague's copy  
on Mac with Tiger.  I can load fasta files from muscle manually using  
menu option but cannot open them with my script.


> I have been using Jalview 2.3 for some time now on an Mac Pro  
> running Leopard and it has worked very well.  Recently I upgraded to  
> Jalview 2.4 and have experienced some strange behavior with fasta  
> files of multiple sequence alignments produced by the Muscle  
> alignment program.
>
> With Jalview 2.3 (labelled May 2007, version 12.2.0), I have no  
> trouble either opening these files via the menu or by calling a  
> script which executes the jar file with the alignment fasta file  
> plus an automatically generated features file as arguments.  When I  
> upgraded to Jalview 2.4 (labelled Sept 16, 2008, version 12.2.0) and  
> tried to run my script from the command line,  I get an error  
> message stating:
>
> Couldn't load xxxxx.fa.muscle
> Formats currently supported are Fasta, MSF, Clustal, BLC, PIR, MSP  
> and PFAM
>
> If I tried to manually select this same file from the menu, Jalview  
> just hangs on "loading...".
>
> I then went back to Jalview 2.3 (I have both 2.3 and 2.4  
> installed).  I could no longer view the files from my script,  
> getting the Couldn't load error message.  But I could load them via  
> the menu option.  I kept going back and forth between 2.4 and 2.3 to  
> trouble shoot. Seemingly randomly,  2.3 would work again with the  
> script.  I could never get 2.4 to work.
>
> I should mentioned that I uninstalled 2.3 (using the uninstall  
> option), installed 2.4 (using install.app).  When 2.4 didn't work, I  
> used Time Machine to get 2.3 back and rename the 2.4 directory in  
> the Applications folder.
>
> I also have a clean version of 2.4 on my laptop which I installed a  
> few months ago.  This version is labelled Aug 27 2008 rather than  
> September.  It works fine on the same files - both via the script  
> and by manually loading the files from the menu.  The laptop is a  
> Macbook Air running the same version of Leopard (10.5.7).
>
> A colleague did a clean install of 2.4 (I think the same version as  
> on my laptop) on a Mac with Tiger and he also cannot use the script  
> but he can manually load the files.
>
> I am completely at a loss to explain this behavior.  Has anyone else  
> suffered from similar problems?  Any solutions?
>

Judith Cohn

--------------------

Judith Cohn, Ph.D.
Information Science (CCS-3)
Mail Stop B256
Los Alamos National Lab
Los Alamos, NM 87545
phone:  505-665-0999
email:  jcohn at lanl.gov



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