[Bioperl-l] RepeatMasker

[Robert Hubley]

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?
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>