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Chris Fields | 1 Aug 04:22
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Re: Bio::Moose is now....

I think, before any CPAN release, I want to nip the monolith in the  
bud.  Just have Meta/Root and simple interfaces (roles) describing  
classes in Biome, actual implementations or other additions going into  
BiomeX::*.  The current Biome::Location/Annotation/etc would  
eventually be moved into their own BiomeX repos.  Bundle with  
Task::Biome (maybe add some automated bundling options).  Sound  
familiar?

I'll try to get a ROADMAP up next week.

chris

On Jul 31, 2009, at 9:53 AM, Robert Buels wrote:

> I think this sounds great.  GREAT news about the Biome::PrimarySeq  
> performance.
>
> Rob
>
> Chris Fields wrote:
>> Biome!  This makes the most sense to me; as Mark points out the  
>> name works as an appropriate acronym (BioPerl with Metaclass  
>> Extensions), as well as a biome being (per wikipedia):
>> "a climatically and geographically defined areas of ecologically  
>> similar climatic conditions such as communities of plants, animals,  
>> and soil organisms ... often referred to as ecosystems".
>> Seems a fitting name for a open-source project.  I'll be moving the  
>> namespace over to Biome over the next couple of days on github.   
>> Now I owe Mark some beer...
>> Now, for extensions, should I assume this will eventually be
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Jonathan Cline | 1 Aug 05:24
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Module issue with cygwin-perl vs. Activestate Perl

I recently mentioned working on Bio::Robotics for Tecan.  Vendors
being MS-Win specific, the vendor software allows third-party software
communication through a named pipe (the literal filename is
"\\\\.\\pipe\\gemini" where the multiple front slashes are MS specific
and this pseudo-pipe is opened with sysopen() ).  This is broken under
cygwin-perl due to cygwin's method of handling paths -- the sysopen
fails.  However it works under ActiveState Perl and communication
through the named pipe (to the robot hardware) is OK.  The standard
workaround is usually to use cygwin bash, and force the PATH to use
ActiveState perl.  (Typical MS Windows incompatibility problem.)  The
issue is:  Perl module libraries for CPAN work under cygwin-perl
(only?).  Attempts to run "activestate-perl Makefile.PL" for CPAN
module use, or "make test", result in a bad list of incompatibility
problems.  Yet ActiveState Perl is required for communicating to the
vendor application (unless there is some workaround to raw filesystem
access in cygwin-perl that I haven't found in 2 days of working this).
  The stand-alone scripts I have work fine to access the named pipe
(using ActiveState Perl) since the standalone scripts have no module
INC dependencies, no CPAN module test harness, etc etc.

This isn't specifically a Bio:: issue, though if anyone has
suggestions please email.  I could try msys and see if it handles the
named-pipe-special-file better, if msys has an msys-perl distribution.

--

-- 
## Jonathan Cline
## jcline <at> ieee.org
## Mobile: +1-805-617-0223
########################
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Mark A. Jensen | 1 Aug 05:50
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Re: Module issue with cygwin-perl vs. Activestate Perl

Jonathan-

I have an utter kludge for this very problem, if I
understand it correctly. The kludge works for
me a majority of the time. Be warned that this
is in no way optimized or clever; there is no warranty
expressed or implied...

Two scripts are below; one runs the other. Together
they convert a makefile generated by ActiveState 
into one suitable for a cygwin make. When the 
cygwin make is run after conversion, the installation
occurs in the ActiveState locations. A demo session
follows (note that 'asperl' is an alias, defined as

 alias asperl=/cygdrive/c/Perl/bin/perl

)
cygwin session:

 $ wget http://search.cpan.org/CPAN/authors/id/N/NI/NI-S/Devel-Leak-0.03.tar.gz
 $ tar -xzf Devel-Leak-0.03.tar.gz
 $ cd Devel-Leak-0.03
 $ asperl Makefile.PL
 $ as2cyg.sh
 $ make
 $ make test
 $ make install

This is how I constantly install CPAN modules "by hand"
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Mark A. Jensen | 1 Aug 06:35
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Re: Module issue with cygwin-perl vs. Activestate Perl

Sorry, I cut off the last script. The entire thing follows:

/usr/local/bin/conv-ASMake.sh :

#!/usr/bin/sed -f
#converting an ActiveState PERL Makefile to run under cygwin make:
s/^DIRFILESEP = ^\\/DIRFILESEP = \//
s/^NOOP = rem/NOOP = :/
# -or- NOOP = echo -n
# byebye volume
s/C:/\/cygdrive\/c/
# sed to convert directory \ to /
s/\([\)0-9a-zA-Z.]\)\\\([\(0-9a-zA-Z]\)/\1\/\2/g
# convert full perl
s/\/usr\/bin\/perl/\/cygdrive\/c\/Perl\/bin\/perl/

# a key conversion for DOC_INSTALL action
/^DESTINSTALLVENDORHTMLDIR/ a\
DECYGDESTINSTALLARCHLIB = $(subst /cygdrive/c,c:,$(DESTINSTALLARCHLIB))

# --- MakeMaker tools_other section:
# let cygwin do native linux commands
/^MAKE/ c\
MAKE = make
/^CHMOD/ c\
CHMOD = chmod
/^CP/ c\
CP = cp
/^MV/ c\
MV = mv
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Jonathan Cline | 3 Aug 05:32
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Re: Bio::Robotics namespace discussion

Smithies, Russell wrote:
> I "acquired" an old Biomek 1000 that I'm thinking of modernising. It was originally controlled by a
monstrously large but slow pc (IBM Value Point Model 466DX2 computer with Microsoft Windows* Version 3.1)
> My plan is to fit a 3-axis CAD/CAM stepper controller (about $60) and use software like mach3
www.machsupport.com along with G-code to control it.
> I come from an engineering background so it seemed like the easy way to me :-)
>
> Now I just need a bit of free time to get it working...
>
> --Russell
>
>
>   
I agree, that's probably the best way to go.  It's hard to know what
amount of s/w processing was done on the host PC vs. the embedded
controller.  If you were able to connect directly to the robot hardware
with serial port(s) or whatever it's using, it would be tough to find
out the comm protocol unless someone has already reverse engineered it
(which is doubtful).   Also from what I have seen online, attempting to
run the old software under virtual machine is unpredictable due to
timing differences in the serial port communication.   So removal of the
old electronics is probably the best bet.  If it has one arm, then it's
much easier.  

As for robots with working workstation software, it seems the annoyance
factor is that while the scripting languages are powerful (for GUI
scripting that is), they are still relatively low level.  Bio types with
a bit of CS seem to immediately turn to visual basic, labview, or even
excel spreadsheets and macros, in order to provide a higher level
abstraction for the workstation software.   To me, it seems natural that
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Dan Bolser | 4 Aug 14:03
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Re: problem with t/LocalDB/SeqFeature.t when host ne localhost

2009/7/31 Chris Fields <cjfields <at> illinois.edu>:
> Dan,
>
> Can you file this as a BioPerl bug?  I'm planning on driving towards
> releasing 1.6.1 alpha1 soon (next few weeks) and I would like to get this
> one fixed.

http://bugzilla.open-bio.org/show_bug.cgi?id=2899

Dan.
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Dan Bolser | 4 Aug 14:14
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Re: Clear range from Bio::Seq::Quality?

2009/4/27 Heikki Lehvaslaiho <heikki.lehvaslaiho <at> gmail.com>:
> Dan,
>
> Have a look at Bio/Seq/Quality.pm and t/Seq/Quality.t in bioperl-live.
>
> Test and extend,
>
>    -Heikki

Thanks for help with this. I finally got round to looking at the code
(after several others had done the same). I have messed with the code
a bit, and added a 'mask_below_threshold' method [1] and some tests to
go with it (including some extra tests) [2].

Cheers,
Dan.

[1] http://bugzilla.open-bio.org/show_bug.cgi?id=2897
[2] http://bugzilla.open-bio.org/show_bug.cgi?id=2898

> 2009/4/27 Heikki Lehvaslaiho <heikki.lehvaslaiho <at> gmail.com>:
>> Dan,
>>
>> I'll take your code and put it into bioperl-live rewritten the way I
>> suggested and add few tests.
>>
>> That should get you started,
>>
>>   -Heikki
>>
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Dan Bolser | 4 Aug 18:32
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Re: Percentage Similarity

2009/7/28 shalabh sharma <shalabh.sharma7 <at> gmail.com>:
> Hi All,          I have some protein sequences (around 100) i need to find
> overall percentage similarity between them.
> How i can do that?

Tried using blast?

You can download that.

Try asking in irc://irc.freenode.net/#bioinformatics

Dan.

>
> Thanks
> Shalabh
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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K. Shameer | 4 Aug 18:43
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Re: Percentage Similarity

Hello Shalabh,

You may try ALISTAT. Available as a part of SQUID library from Prof. Sean
Eddy. Make an alignment of your 100 sequences and use alignment as input
of ALISTAT. ftp://selab.janelia.org/pub/software/squid/

Best,
Khader Shameer

> 2009/7/28 shalabh sharma <shalabh.sharma7 <at> gmail.com>:
>> Hi All,          I have some protein sequences (around 100) i need to
>> find
>> overall percentage similarity between them.
>> How i can do that?
>
> Tried using blast?
>
> You can download that.
>
>
> Try asking in irc://irc.freenode.net/#bioinformatics
>
> Dan.
>
>
>>
>> Thanks
>> Shalabh
>> _______________________________________________
>> Bioperl-l mailing list
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shalabh sharma | 4 Aug 19:36
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Re: Percentage Similarity

Hi All,       thanks a lot.
@Khader Shameer, ALISTAT is what i was looking for. But still it gives you
the average identity, what i need exactly is the average similarity.

Thanks
Shalabh Sharma

On Tue, Aug 4, 2009 at 12:43 PM, K. Shameer <shameer <at> ncbs.res.in> wrote:

> Hello Shalabh,
>
> You may try ALISTAT. Available as a part of SQUID library from Prof. Sean
> Eddy. Make an alignment of your 100 sequences and use alignment as input
> of ALISTAT. ftp://selab.janelia.org/pub/software/squid/
>
> Best,
> Khader Shameer
>
> > 2009/7/28 shalabh sharma <shalabh.sharma7 <at> gmail.com>:
> >> Hi All,          I have some protein sequences (around 100) i need to
> >> find
> >> overall percentage similarity between them.
> >> How i can do that?
> >
> > Tried using blast?
> >
> > You can download that.
> >
> >
> > Try asking in irc://irc.freenode.net/#bioinformatics
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Gmane