[Bioperl-l] RepeatMasker

[Chris Fields]

Thanks for the update Robert!

chris

On Jul 14, 2009, at 2:42 PM, Robert Hubley wrote:

> Hi Chris,
>
> Just got back from a conference.
> So the original problem reported ( "Exception ( no such file or  
> directory )" ) caused by:
>
> "Cause: mysequence.masked file (which holds the masked sequence) not  
> found when
>   no repeats are found in the supplied sequence. This file is not  
> created anymore
>   when no repeats are found."
>
> This is still the case, with RepeatMasker at least.  We no longer  
> create a *.masked file when no repeats are located in the input  
> file.  This can be checked by looking at the *.out file which in  
> these cases will contain only one line:
>
> "There were no repetitive sequences detected in ...<filename>..."
>
>
> In comment #1 of this bugreport a user writes:
>
>  "This may be related to a bug with RepeatMasker and is known to be  
> an issue with
>    BioPerl:
>
>    http://www.bioperl.org/wiki/Release_1.5.2#Notes
>
>   The RepeatMasker authors have been notified about this and  
> hopefully will have
>   a fix available soon.  The question now is, should RepeatMasker.pm  
> check for no
>   returned results?"
>
> This refers to a bug in the option processing in RM Version 3.1.6  
> ( '-noint' etc. ).  This was fixed
> in 3.1.7 and has not returned.  So this should no longer be  
> impacting any version of bioperl.
>
> -R
>
>
>
>
> Chris Fields wrote:
>> Robert,
>>
>> Sorry about that last post, thought you were reporting a problem  
>> not inquiring about one.
>>
>> Here's what we have:
>>
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2138
>>
>> Not sure but from the last few reports this is still a problem with  
>> RepeatMasker and bioperl.  I'll try looking into it from our end.
>>
>> chris
>>
>> On Jul 7, 2009, at 8:58 AM, Robert Hubley wrote:
>>
>>> This list email as forwarded to us by a colleague.  I fixed this  
>>> bug awhile back and I just double checked 3.2.8 and don't see any  
>>> problems with the options -noint or -lcambig.  Could someone help  
>>> us determine how this is breaking bio-perl?
>>>
>>> Thanks,
>>>
>>> -Robert
>>>
>>> |We have told the guys at RepeatMasker that RM-3.1.6 have a problem
>>> |causing Bio::Tools::RepeatMasker to crash in November 2006 (Bug  
>>> 2138).
>>> |And as of today, they are now at 3.2.8, and the problem is not  
>>> fixed.
>>> |And I don't want my project to be stalled-- any tips for a  
>>> workaround?
>>> ||
>>> ||Hi,
>>> ||
>>> ||Perhaps you already know about this, but in RepeatMasker 3.1.6 - 
>>> noint ||cannot be used because of error 'Unknown option: noint- 
>>> species'.
>>> ||This is caused by line 1131 having no space after the "-noint".  
>>> ||Likewise, -lcambig on 1128 would probably suffer a similar  
>>> problem.
>>> ||
>>> ||Will this be fixed in the next version, and how often do you  
>>> release new ||versions?
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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