Chris Fields | 1 Feb 20:03 2008
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Odd issue with HSP::seq_inds()

Apologies ahead of time for the longish post!

While working on a recent bug (http://bugzilla.open-bio.org/show_bug.cgi?id=2436 
) I found a pretty significant bug.  It appears that seq_inds() is  
giving some bad return values tied specifically to reports where  
either or both query or hit are translated.  I'll file a full bug  
report but I felt it might be worth bringing up here to discuss  
specifically what values should be expected when these reports are  
parsed (all three nucleotide positions or only the first for each  
nonmatching translated position, etc).

I used the following script to track the total HSPs as well as those  
where seq_inds() returns positions within the HSP bounds for query and  
hit:

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

use Bio::SearchIO;
use Test::More qw(no_plan);

my $file = shift || die;

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

my ($hsp_co, $correctq, $correcth) = (0,0,0);

while (my $res = $io->next_result) {
     while (my $hit = $res->next_hit) {
         while (my $hsp = $hit->next_hsp) {
(Continue reading)

Terrance Mok | 3 Feb 22:54 2008
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Problems Installing Bioperl 1.5.2 - Windows

Hi I've been trying to install bioperl on a fresh install of ActivePerl on
Windows.
Following the installation guide using the GUI Perl Package Manager, I add
the 4 locations and all of them list 0 packages except for "Bribes
http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>".
Then when searching for bioperl (with all package view), nothing shows up
since no packages are found for all the other locations I added.

I've also had problems installing on Ubuntu (helping a friend), when using
CPAN and following exactly the guide on the bioperl installation it will not
work.  When doing the install command in CPAN, install S/SE/SENDU/bioperl-
1.5.2_102.tar.gz  she gets an error that
"/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at
Makefile.PL line 25."
ANJAN PURKAYASTHA | 3 Feb 18:10 2008
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sequence object question

hi,
here is the problem i'm facing.

i parse a genbank file with the statement:
my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format =>
'GenBank');
while (my $seq_obj= $gb_stream->next_seq){
.....

}

presumably $seq_obj is a Bio::Seq::RichSeq object.

now, when I try:
my $feat_obj($seq_obj->getSeqFeatures){
.....
}
i get an error message: Can't locate object method "getSeqFeatures" via
package "Bio::Seq::RichSeq" at gb_file_reader.pl line 11.

on reading docs I find that Bio::Seq::RichSeq does not have a getSeqFeatures
method.
but, RIchSeq is a child of the Seq class, which HAS a getSeqFeatures method
(i presume this method is also inherited by the RichSeq class).

so, why am i getting an error message and how do i go about getting the
features within each genbank file?

appreciate any pointers.

(Continue reading)

Jason Stajich | 4 Feb 00:51 2008

Re: sequence object question

It is 'get_SeqFeatures'
http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1

Deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio 
%3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq
http://bioperl.org/cgi-bin/deob_detail.cgi? 
method=Bio::Seq::get_SeqFeatures

HOWTO:
http://bioperl.org/wiki/HOWTO:Feature-Annotation

On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote:

> hi,
> here is the problem i'm facing.
>
> i parse a genbank file with the statement:
> my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format =>
> 'GenBank');
> while (my $seq_obj= $gb_stream->next_seq){
> .....
>
> }
>
> presumably $seq_obj is a Bio::Seq::RichSeq object.
>
> now, when I try:
> my $feat_obj($seq_obj->getSeqFeatures){
> .....
(Continue reading)

ANJAN PURKAYASTHA | 4 Feb 05:00 2008
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Re: sequence object question

Thanks a lot!

On Feb 3, 2008 6:51 PM, Jason Stajich <jason <at> bioperl.org> wrote:

> It is 'get_SeqFeatures'
> http://doc.bioperl.org/bioperl-live/Bio/FeatureHolderI.html#POD1
>
> Deobfuscator:
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio
> %3A%3ASeq&sort_order=by+method&search_string=Bio%3A%3ASeq
> http://bioperl.org/cgi-bin/deob_detail.cgi?
> method=Bio::Seq::get_SeqFeatures
>
> HOWTO:
> http://bioperl.org/wiki/HOWTO:Feature-Annotation
>
>
> On Feb 3, 2008, at 9:10 AM, ANJAN PURKAYASTHA wrote:
>
> > hi,
> > here is the problem i'm facing.
> >
> > i parse a genbank file with the statement:
> > my $gb_stream = Bio::SeqIO->new( -file => 'gb_test_file', -format =>
> > 'GenBank');
> > while (my $seq_obj= $gb_stream->next_seq){
> > .....
> >
> > }
> >
(Continue reading)

Sendu Bala | 4 Feb 09:45 2008
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Re: Problems Installing Bioperl 1.5.2 - Windows

Terrance Mok wrote:
> Hi I've been trying to install bioperl on a fresh install of ActivePerl on
> Windows.
> Following the installation guide using the GUI Perl Package Manager, I add
> the 4 locations and all of them list 0 packages except for "Bribes
> http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>".
> Then when searching for bioperl (with all package view), nothing shows up
> since no packages are found for all the other locations I added.

Hopefully someone else will chime in, but perhaps there's something 
wrong with the server? Can anyone else confirm?

> I've also had problems installing on Ubuntu (helping a friend), when using
> CPAN and following exactly the guide on the bioperl installation it will not
> work.  When doing the install command in CPAN, install S/SE/SENDU/bioperl-
> 1.5.2_102.tar.gz  she gets an error that
> "/home/username/.cpan/build/bioperl-1.5.2_102: No such file or directory at
> Makefile.PL line 25."

Hard to figure out what might be wrong without complete details. Can she 
install anything else via CPAN? Has she run out of disc space?
Darren Obbard | 4 Feb 09:56 2008
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Picon

Re: Problems Installing Bioperl 1.5.2 - Windows

Hi,

> Terrance Mok wrote:
>> Then when searching for bioperl (with all package view), nothing 
>> shows up
>> since no packages are found for all the other locations I added.
> Hopefully someone else will chime in, but perhaps there's something 
> wrong with the server? Can anyone else confirm?
Just to note that I too have had the same problem. From ca. 2 weeks ago 
I could see no packages on the recommended bioperl repository. I just 
assumed I was doing something wrong, and thought I'd wait until my need 
became urgent.

--

-- 

Darren Obbard
University of Edinburgh, UK
Darren Obbard | 4 Feb 12:07 2008
Picon
Picon

Re: Problems Installing Bioperl 1.5.2 - Windows

Hi again,

Having just looked, it seems fine on this machine (XP proffessional, 
sp2). The problem I was (and am) having are on a clean install of Vista 
(ultimate).

Perhaps this is a vista/activestate issue? What versions of 
windows/activeperl are people having problems with?
Chris Fields | 4 Feb 18:53 2008
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Re: Problems Installing Bioperl 1.5.2 - Windows


On Feb 4, 2008, at 2:45 AM, Sendu Bala wrote:

> Terrance Mok wrote:
>> Hi I've been trying to install bioperl on a fresh install of  
>> ActivePerl on
>> Windows.
>> Following the installation guide using the GUI Perl Package  
>> Manager, I add
>> the 4 locations and all of them list 0 packages except for "Bribes
>> http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>".
>> Then when searching for bioperl (with all package view), nothing  
>> shows up
>> since no packages are found for all the other locations I added.
>
> Hopefully someone else will chime in, but perhaps there's something  
> wrong with the server? Can anyone else confirm?

I haven't used ActivePerl in a while personally since switching to OS  
X (even when using perl 5.10).  Terrance, did you follow the  
ActivePerl instructions or our installation instructions?  Also, we  
don't guarantee that it will work with AtcivePerl's 5.10 port but it's  
worth a try; if not downgrade to the latest 5.8 build.

>> I've also had problems installing on Ubuntu (helping a friend),  
>> when using
>> CPAN and following exactly the guide on the bioperl installation it  
>> will not
>> work.  When doing the install command in CPAN, install S/SE/SENDU/ 
>> bioperl-
(Continue reading)

Jay Hannah | 4 Feb 20:42 2008
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SVN server trouble?

I'm getting this error trying to check out trunk, from 2 different 
servers on 2 different networks:

$ svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live
svn: Can't find a temporary directory: Error string not specified yet

Is this an SVN server problem of some sort, or is it just me somehow?

(
   Oh, and come hang out with us: 
      irc.freenode.net #bioperl
)

Thanks,

Jay Hannah
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah

Gmane