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Philip Lijnzaad | 3 Dec 2002 16:00
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bug in location->to_FTstring

Dear all, 

hope you're all doing well!  Quick question. I installed bioperl-1.0.2 from
CPAN, and noticed what looks like a rather serious bug in 

Bio::Location (or Bio::Location::Split). When I read the following file:
------------------------------------------------------------------------
ID   foo
AC   bar
XX
FH   Key             Location/Qualifiers
FH
FT   gene            complement(1..20)
FT                   /gene="YJL225C"
FT   CDS             complement(join(1..4,10..20))
FT                   /gene="YJL225C"
SQ   Sequence 60 BP; 15 A; 15 C; 15 G; 15 T; 0 other;
     cccacacaca caccacaccc acacccacac acaccacacc cacacaccac acccacacca        60
//
------------------------------------------------------------------------

and iterate over the features to extract the locations, like so:

  for my $feat ( $seq->top_SeqFeatures ) { 
  # $feat is a Bio::SeqFeature::Generic
    print $loc=$feat->location->to_FTstring;
  } 

It prints
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Ewan Birney | 3 Dec 2002 16:30
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Re: Pushing towards 1.2

On Tue, 3 Dec 2002, Jason Stajich wrote:

> I would also suggest looking at the bugs in the list and deciding which
> ones will be fixed before the release, some of these have been hanging
> around for a while...

Yup - are the bugs distributed between jitterbug and bugzilla? I thought 
the jitterbug bugs looked ok. On my list...

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

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney <at> ebi.ac.uk>. 
-----------------------------------------------------------------
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Viren Konde | 3 Dec 2002 16:53
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Re: All roads lead to Bio::Seq

Yes, pretty easy to understand and Thanks.

-------------
Viren Konde, PhD
Postdoc, Univ. of Houston,
Dept. Biol. and Biochem.
TX 77204, USA.

Date: Tue, 03 Dec 2002 09:47:19 -0500
From: Lincoln Stein <lstein <at> cshl.org>
Subject: Re: [Bioperl-l] All roads lead to Bio::Seq
To: Ewan Birney <birney <at> ebi.ac.uk>,
bioperl-l <at> bioperl.org
Reply-to: lstein <at> cshl.org
Organization: Home

Looks good to me.

Lincoln

On Monday 02 December 2002 01:10 pm, Ewan Birney
wrote:
> I will soon commit this which is reorganise the
documentation in
> Bio::Seq, Bio::SeqI, Bio::PrimarySeqI and
Bio::PrimarySeq to stress
> that Bio::Seq has the best documentation and
starting point for users
> of the package. I am also using [Developers] in the
=head1 NAME line
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James Wasmuth | 3 Dec 2002 17:44
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HSP brain rot...

Hi all,

I'm using Bio::SearchIO and having problems determining which sequence I 
want to use the methods on.  The documentation states 'hit' & 'query' 
but if I use these I one of hit or query displayed, if I type nothing 
then I get the default...  

my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => "$infile");

while( my $result = $in->next_result ) {
    my $query = $result->query_name;
    print "\n\nQueried sequence: $query\n";

    while( my $hit = $result->next_hit ) {
            while( my $hsp = $hit->next_hsp ) {
                print $hsp->start('hit'),"\t", $hsp->end('hit') ,"\n";
                ...

could someone cure my Tuesday afternoon blues...  :o)

many thanks...

James
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Jason Stajich | 3 Dec 2002 18:18

Re: Pushing towards 1.2

bugs are only on bugzilla.  jitterbug should be dead - chris can we kill
the bugs-email alias somehow - I was hoping someone could set it up so it
would still create bugs...

 On Tue, 3 Dec 2002, Ewan Birney wrote:

> On Tue, 3 Dec 2002, Jason Stajich wrote:
>
> > I would also suggest looking at the bugs in the list and deciding which
> > ones will be fixed before the release, some of these have been hanging
> > around for a while...
>
> Yup - are the bugs distributed between jitterbug and bugzilla? I thought
> the jitterbug bugs looked ok. On my list...
>
>
> >
> >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney <at> ebi.ac.uk>.
> -----------------------------------------------------------------
>
(Continue reading)

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Tyler | 3 Dec 2002 19:35
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ProtDist.pm

I'd like to ask Jason or Shawn (or anyone else) whether or not it's 
possible to run ProtDist from two perl scripts (with different process 
ids) at the same time with the same working directory? I've tried 
setting a unique name for the outfiles, yet I still get a message 
saying "protdist did not create matrix correctly" for the script that 
is started second.  I am making the assumption that it is trying to 
write to an outfile that already exists and is in use by the script 
started first, but I can't figure out why!  I'm using version 1.14 from 
the cvs.

(Actually, to be more accurate, it's one script that forks child 
processes that handle client requests. Regardless, the PD* filenames 
are unique.)

Here's a code snippet:
	...
	print $client "STATUS\nCalculating distance matrix...\n";
	my $pdfile = "PD" . $$ . time() . ".out";  #creating a unique filename
	my $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
	$protdist_factory->quiet(1);
	$protdist_factory->outfile_name($pdfile);
	my $matrix;
	eval { $matrix  = $protdist_factory->create_distance_matrix($aln);};  
#$aln created earlier in script
		if ($ <at> ) {
			my $e = $ <at> ;
			$e =~ s/\n/ /;
			print $client "ERROR\n$e\n";
			close($client);
			return "Error: $e";
(Continue reading)

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Jason Stajich | 3 Dec 2002 20:20

Re: ProtDist.pm

We need to change the phylip programs to run in a separate directory per
Factory Object instance.  Right now it is using cwd.
I currently do this for the PAML running - so it shouldn't be too hard to
migrate that back in to the _run function.

The problem is that PHYLIP doesn't allow you to change what the outputfile
name is (grr) so you have to work around this by changing the cwd for
the processes...  So changing outfile_name doesn't do any good - it is
only useful if you have compiled your PHYLIP to use a different
outputfile name or to deal with potential differences in expected
outputfile name between versions of PHYLIP.

Make sense?

If you want to have a go with the code feel free - otherwise I can look
into it in the next few days.

The dumb workaround is to startup your separate ProtDist instances in
different directories, if you are forking in perl I suppose  this
gets hairyer but you can just issue the chdir($tempdir) before
instantiating the new ProtDist object and it should work.

-jason
On Tue, 3 Dec 2002, Tyler wrote:

> I'd like to ask Jason or Shawn (or anyone else) whether or not it's
> possible to run ProtDist from two perl scripts (with different process
> ids) at the same time with the same working directory? I've tried
> setting a unique name for the outfiles, yet I still get a message
> saying "protdist did not create matrix correctly" for the script that
(Continue reading)

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Paul Boutros | 3 Dec 2002 20:46
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Re: Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query]

Hi Lincoln,

I'm a total novice with the PERL debugger, but I took Ewan's suggestion
to play with it, and I seem to have gotten it to pass all
tests.  

The only change I made was:

if (defined $result) {
to
if ($result) {

To be honest I'm not sure why it works, and perhaps I've broken something
else in there?  It just seemed reasonable to me that since you had already
done a
my $result
then
if (defined $result)
would always be true and enter the loop.

Does this help at all?
Paul

On Tue, 3 Dec 2002, Lincoln Stein wrote:

> I've just changed the subject line of this message, since it is haunting me.  
> I'm beginning to fear that we're running into the weird workarounds required 
> to emulate piped I/O under Windows.  I'll try to run bioperl regression tests 
> on my own windows system (haven't done it till now because of inertia -- 
> getting CVS etc)
(Continue reading)

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Lincoln Stein | 3 Dec 2002 21:20

Re: Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query]

Oh, oh, oh.  I see what the problem is.  The "defined" was intentional, but 
I'll have to do a better job with the logic.  Thanks!

Lincoln

On Tuesday 03 December 2002 02:46 pm, Paul Boutros wrote:
> Date:
> Tue, 3 Dec 2002 14:46:32 -0500 (EST)

--

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein <at> cshl.org			                  Cold Spring Harbor, NY
========================================================================
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Lincoln Stein | 3 Dec 2002 21:26

Re: Not done with Bio::DB::Query [WAS: All done with Bio::DB::Query]

Hi Paul,

Try the latest CVS version.  This contains the "correct" fix.

Lincoln

On Tuesday 03 December 2002 02:46 pm, Paul Boutros wrote:
> Hi Lincoln,
>
> I'm a total novice with the PERL debugger, but I took Ewan's suggestion
> to play with it, and I seem to have gotten it to pass all
> tests.
>
> The only change I made was:
>
> if (defined $result) {
> to
> if ($result) {
>
> To be honest I'm not sure why it works, and perhaps I've broken something
> else in there?  It just seemed reasonable to me that since you had already
> done a
> my $result
> then
> if (defined $result)
> would always be true and enter the loop.
>
> Does this help at all?
> Paul
>
(Continue reading)

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Gmane