RepeatMasker

[Robert Hubley]

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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[Chris Fields-5]

Robert, the best way to handle this is to file a bug report indicating  
all the specifics as well as some example code demonstrating the  
problem.

http://www.bioperl.org/wiki/Bugs

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@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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[Chris Fields-5]

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@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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[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?
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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[Chris Fields-5]

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

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