[Bioperl-l] Re: Bioperl-l Digest, Vol 1, Issue 25 (Eric E. Snyder: incommunicado)

Tue May 20 12:06:41 EDT 2003

Dr. Snyder will be unavailable for comment until May 26.

>>> bioperl-l 05/20/03 11:02 >>>

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Today's Topics:

   1. RE: tests failing miserably (Jason Stajich)
   2. Another update for my alignment module (Yee Man Chan)
   3. Root::IO tempfile error (kaboroev at sfu.ca)
   4. Re: Another update for my alignment module (Ewan Birney)
   5. bioperl and Perl (Line Neil)
   6. Re: bioperl and Perl (Jason Stajich)
   7. Re: Re: Another update for my alignment module (Aaron J Mackey)

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

Message: 1
Date: Mon, 19 May 2003 13:19:05 -0400 (EDT)
From: Jason Stajich <jason at cgt.duhs.duke.edu>
Subject: RE: [Bioperl-l] tests failing miserably
To: Hilmar Lapp <hlapp at gnf.org>
Cc: Bioperl <bioperl-l at bioperl.org>
Message-ID:
	<Pine.LNX.4.50.0305191235280.18027-100000 at tenero.duhs.duke.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I've added some changes to Bio::Root::IO which allow one to explicitly
request the IO object to not auto-close a filehandle.

The non-closing fh boolean flag was added to fix problems with the
Index::Blast object b/c we were using a shared filehandle but delegating
it to the a parser to get back a Search object.

I also updated Bio::Index::Blast to use SearchIO instead of BPlite to
parse the report.  For those not familiar with the object, it is useful
if
you have a whole lot of Blast reports which you might imagine storing in
a
single file and giving people access to the raw report, like from a
website, this object gives an easy way to basically index based on query
name so you can jump to that record in the report.

I also fixedRoot::IO to NOT try and close IO::String filehandles as this
causes segfaults (a t/Molphy.t segfault was happening for this).

I think this is particular to a specific version of IO::String but I'm
not
sure - I had the same problems with ChrisM's Data::Stag trying to close
IO::String fh's too.  Something for a perl hacker to investigate I hope.

Root::IO will also not try and close a filehandle if it is STDOUT or
STDERR now.

Finally, I backed out the changes to Bio::TreeIO classes as my first
attempt to parse newick files with labeled internal nodes didn't work
(sorry Mike)  and we'll have to give it another go later on.  This fixes
the Molphy and Tree.t test failures.

-jason

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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

Message: 2
Date: Mon, 19 May 2003 16:29:43 -0700 (PDT)
From: Yee Man Chan <ymc at paxil.stanford.edu>
Subject: [Bioperl-l] Another update for my alignment module
To: Ewan Birney <birney at ebi.ac.uk>
Cc: bioperl-l at bioperl.org
Message-ID:
	<Pine.GSO.3.96.1030519161702.701A-100000 at beacon.stanford.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

Hi Ewan,

	I got another update for my align module. This time I stole some
ideas from the align routine in ssearch to make my code faster. This
makes 
it 9.35% faster than the align routine for ssearch because I am using
gap arrays to represent alignment and I used pointers to walk the Gotoh
arrays. You can find my new code at:

http://www.stanford.edu/~yeeman/dsw.tgz

	I believe my code generates correct alignments because I ran it
through some 1700 pairs of 100kb sequences and it seems to show very
similar result to AVID.

	The search phase used in my algorithm is still Miller-Myers (The
fastest Smith-Waterman that calculates every cell). The search phase
time
can be reduced in half if I replace it by Phil Green's algorithm (an
even 
faster one but it ignores some cells based on some heuristics.). As a
future work, I can add Phil Green's code to my module for people who
want
to sacrifice some sensitivity for speed.

	I think my code is now worthy to be included in bioperl. Can you
tell me how I can go about doing it?

Thanks a lot.
Yee Man

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

Message: 3
Date: Mon, 19 May 2003 17:44:09 -0700
From: kaboroev at sfu.ca
Subject: [Bioperl-l] Root::IO tempfile error
To: bioperl-l at bioperl.org
Message-ID: <200305200044.h4K0i9Zn015287 at rm-rstar.sfu.ca>
Content-Type: text/plain

Hi all,
i have a script that uses both the Standalone blast and Lagan wrappers
for
pairwise alignments.  However, every so often (varies when it will
occur) i
receive an error that the temp file for one of the input sequences
cannot be
found.	i have the error for the lagan below.  also if i get around the
throw (catch with an eval {}) and continue, the next instance of an
alignment does not necessarily fail.  Also, if the suggested remedy is
update my bioperl, when i install the second copy (from a non-root
account)
how do i ensure that the the newer version of the modules are used (I'm
asking because i already tried and could not force my scripts to use
those
modules located in my home directory)

keith
==============================
==============================
Use of uninitialized value in -e at /home/boroevich/perllib/Lagan.pm
line
440 (#2)
    (W uninitialized) An undefined value was used as if it were already
    defined.  It was interpreted as a "" or a 0, but maybe it was a
mistake.

    To suppress this warning assign a defined value to your variables.

    To help you figure out what was undefined, perl tells you what
operation

    you used the undefined value in.  Note, however, that perl optimizes
your
    program and the operation displayed in the warning may not
necessarily
    appear literally in your program.  For example, "that $foo" is
    usually optimized into "that " . $foo, and the warning will refer to
    the concatenation (.) operator, even though there is no . in your
    program.

Uncaught exception from user code:

------------- EXCEPTION  -------------
MSG: Could not open /tmp/900CWxCW1G for reading: No such file or
directory
STACK Bio::Root::IO::_initialize_io
/usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm:260
STACK Bio::AlignIO::_initialize
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:389
STACK Bio::AlignIO::new
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:325
STACK Bio::AlignIO::new
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm:338
STACK Lagan::_runlagan /home/boroevich/perllib/Lagan.pm:410
STACK Lagan::_generic_lagan /home/boroevich/perllib/Lagan.pm:328
STACK Lagan::lagan /home/boroevich/perllib/Lagan.pm:207
STACK toplevel ./update_alignments:214

--------------------------------------
	Bio::Root::Root::throw('Bio::AlignIO::fasta=HASH(0x9f597fc)',
'Could
not open /tmp/900CWxCW1G for reading: No such file or dire...') called
at
/usr/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm line 260
	Bio::Root::IO::_initialize_io('Bio::AlignIO::fasta=HASH(0x9f597fc)',
'-file', '/tmp/900CWxCW1G', '-format', 'fasta') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm line 389
	Bio::AlignIO::_initialize('Bio::AlignIO::fasta=HASH(0x9f597fc)',
'-file', '/tmp/900CWxCW1G', '-format', 'fasta') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm line 325
	Bio::AlignIO::new('Bio::AlignIO::fasta', '-file',
'/tmp/900CWxCW1G',
'-format', 'fasta') called at
/usr/lib/perl5/site_perl/5.6.1/Bio/AlignIO.pm
line 338
	Bio::AlignIO::new('Bio::AlignIO', '-file', '/tmp/900CWxCW1G',
'-format', 'fasta') called at /home/boroevich/perllib/Lagan.pm line 410
	Lagan::_runlagan('Lagan=HASH(0x9f4bc08)', 'lagan.pl', ' -order
"-gs
-7 -gc -2 -mt 2 -ms -1"  -recurse "(12,0,25,0),(13,...',
'/tmp/FoEbuF3Gzc',
'/tmp/lIXp1wXIvh') called at /home/boroevich/perllib/Lagan.pm line 328
	Lagan::_generic_lagan('Lagan=HASH(0x9f4bc08)', 'lagan.pl',
'/tmp/FoEbuF3Gzc', '/tmp/lIXp1wXIvh') called at
/home/boroevich/perllib/Lagan.pm line 207
	Lagan::lagan('Lagan=HASH(0x9f4bc08)',
'Bio::PrimarySeq=HASH(0x9f5dc3c)', 'Bio::PrimarySeq=HASH(0x9f59acc)')
called
at ./update_alignments line 214

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

Message: 4
Date: Tue, 20 May 2003 06:51:17 +0100 (BST)
From: Ewan Birney <birney at ebi.ac.uk>
Subject: [Bioperl-l] Re: Another update for my alignment module
To: Yee Man Chan <ymc at paxil.stanford.edu>
Cc: bioperl-l at bioperl.org
Message-ID:
	<Pine.OSX.4.44.0305200650111.12782-100000 at ewan-birneys-computer.local>
Content-Type: TEXT/PLAIN; charset=US-ASCII

>
> 	I think my code is now worthy to be included in bioperl. Can you
> tell me how I can go about doing it?
>

Someone needs to look at how well it binds to bioperl objects in terms
of
bioperl-ext - probably that is either Aaron or me. Aaron - do you have
time to look at this or should I do this?

> Thanks a lot.
> Yee Man
>
>

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

Message: 5
Date: Tue, 20 May 2003 15:29:09 +0200
From: Line Neil <line.neil at millegen.com>
Subject: [Bioperl-l] bioperl and Perl
To: bioperl-l at bioperl.org
Message-ID: <0990D68E-8AC7-11D7-B9EA-000A959C4E7E at millegen.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed

I am working on Mac OSX 10.2 and I have apparently a problem after 
installation of Perl-5.8 to install Bioperl; is there a bug, is it 
better to reinstall Perl-5.6 for this Bioperl because I need it 
absolutely.

Thanks in advance

Cordially

Line

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

Message: 6
Date: Tue, 20 May 2003 09:36:05 -0400 (EDT)
From: Jason Stajich <jason at cgt.duhs.duke.edu>
Subject: Re: [Bioperl-l] bioperl and Perl
To: Line Neil <line.neil at millegen.com>
Cc: bioperl-l at bioperl.org
Message-ID:
	<Pine.LNX.4.50.0305200935530.20787-100000 at tenero.duhs.duke.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

and the bug,error message is...

On Tue, 20 May 2003, Line Neil wrote:

> I am working on Mac OSX 10.2 and I have apparently a problem after
> installation of Perl-5.8 to install Bioperl; is there a bug, is it
> better to reinstall Perl-5.6 for this Bioperl because I need it
> absolutely.
>
> Thanks in advance
>
> Cordially
>
> Line
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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

Message: 7
Date: Tue, 20 May 2003 11:53:13 -0400 (EDT)
From: Aaron J Mackey <ajm6q at virginia.edu>
Subject: Re: [Bioperl-l] Re: Another update for my alignment module
To: Ewan Birney <birney at ebi.ac.uk>
Cc: Yee Man Chan <ymc at paxil.stanford.edu>, bioperl-l at bioperl.org
Message-ID:
	<Pine.OSF.4.33.0305201151120.20230-100000 at alpha10.bioch.virginia.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII

I'd say yes, but I don't want to hold anyone up.  Better probably to air
this out in the public, so that anyone can jump in.

What's our status with Bio::Matrix for similarity matrices and/or
profiles?  Yee, can you post some sample "SYNOPSIS"-type perl code that
shows how one would use your stuff from "bioperl-space".

Thanks,

-Aaron

On Tue, 20 May 2003, Ewan Birney wrote:

>
>
> >
> > 	I think my code is now worthy to be included in bioperl. Can you
> > tell me how I can go about doing it?
> >
>
> Someone needs to look at how well it binds to bioperl objects in terms
of
> bioperl-ext - probably that is either Aaron or me. Aaron - do you have
> time to look at this or should I do this?
>
>
>
> > Thanks a lot.
> > Yee Man
> >
> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu

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

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End of Bioperl-l Digest, Vol 1, Issue 25
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