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Mark A. Jensen | 2 Nov 05:47
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annotations

I'm cogitating on features and annotations. For a RichSeq, one gets the set of annotations by

$seq->annotation->get_Annotations

while getting features by 

$seq->get_Features

Is there a reason not to have a method in SeqI 

sub get_Annotations { shift->annotation->get_Annotations }

to allow a user to do what seems natural from a user's perspective, viz. $seq->get_Annotations? I imagine
this might save hundreds of hours of frustration, integrated over all newbies.
MAJ
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Chris Fields | 2 Nov 14:08
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Re: annotations

On Nov 1, 2009, at 10:47 PM, Mark A. Jensen wrote:

> I'm cogitating on features and annotations. For a RichSeq, one gets  
> the set of annotations by
>
> $seq->annotation->get_Annotations
>
> while getting features by
>
> $seq->get_Features
>
> Is there a reason not to have a method in SeqI
>
> sub get_Annotations { shift->annotation->get_Annotations }
>
> to allow a user to do what seems natural from a user's perspective,  
> viz. $seq->get_Annotations? I imagine this might save hundreds of  
> hours of frustration, integrated over all newbies.
> MAJ

One could add the methods to delegate to annotation() (that's  
essentially what I'm planning on doing for Biome).

chris
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Kie Kyon Huang | 3 Nov 16:14
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render_blast problem

Hi,

I was trying to follow the HOWTO:Graphics at
http://www.bioperl.org/wiki/HOWTO:Graphics

When running the command line in cygwin

$ perl render_blast1.pl data1.txt | display -

I get the following error line,

bash: display: command not found

I also tried

$ perl render_blast1.pl data1.txt > data1.png

however, I was unable to open the data1.png file using Microsoft
Office Picture Manager or windows Photo Gallery

Thanks

Huang
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Peter | 3 Nov 16:45
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Re: render_blast problem

On Tue, Nov 3, 2009 at 3:14 PM, Kie Kyon Huang <kiekyon.huang <at> gmail.com> wrote:
> Hi,
>
> I was trying to follow the HOWTO:Graphics at
> http://www.bioperl.org/wiki/HOWTO:Graphics
>
> When running the command line in cygwin
>
> $ perl render_blast1.pl data1.txt | display -
>
> I get the following error line,
>
> bash: display: command not found

That makes sense on Windows, since display is a Unix
command line tool.

> I also tried
>
> $ perl render_blast1.pl data1.txt > data1.png

Based on the wiki, I think that ought to have worked.

> however, I was unable to open the data1.png file using Microsoft
> Office Picture Manager or windows Photo Gallery

Did you do this step?:
>> Important!  If you are on a Windows platform, you need to put
>> STDOUT into binary mode so that the PNG file does not go
>> through Window's carriage return/linefeed transformations.
(Continue reading)

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Peter | 3 Nov 17:04
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Re: render_blast problem

Mailing list CC'd - solved :)

On Tue, Nov 3, 2009 at 3:55 PM, Kie Kyon Huang <kiekyon.huang <at> gmail.com> wrote:
>
> ok, that fix it
> i forget sometimes what platform am i on.
> thanks

Great.

Peter
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Aaron Mackey | 3 Nov 18:09
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svn errors?

[ajm6q <at> lc4 bioperl-live]$ svn update
svn: Decompression of svndiff data failed

I'll admit to not having svn updated in awhile; A clean, anonymous svn co
failed with the same message:

[...]
A    bioperl-live/Bio/Structure/StructureI.pm
A    bioperl-live/Bio/Structure/IO
svn: Decompression of svndiff data failed

-Aaron

P.S. I used this command: svn co svn://
code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live
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Chris Fields | 3 Nov 18:17
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Re: svn errors?

Aaron,

Yep, this was reported to support (a couple of users on #bioperl  
reported the same problem).  Chris D. is looking into it.

I'm wondering if it's worth setting up a second mirror to github for  
this purpose.

chris

On Nov 3, 2009, at 11:09 AM, Aaron Mackey wrote:

> [ajm6q <at> lc4 bioperl-live]$ svn update
> svn: Decompression of svndiff data failed
>
>
> I'll admit to not having svn updated in awhile; A clean, anonymous  
> svn co
> failed with the same message:
>
> [...]
> A    bioperl-live/Bio/Structure/StructureI.pm
> A    bioperl-live/Bio/Structure/IO
> svn: Decompression of svndiff data failed
>
> -Aaron
>
> P.S. I used this command: svn co svn://
> code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live
> _______________________________________________
(Continue reading)

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Chris Fields | 3 Nov 18:19
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Re: render_blast problem


On Nov 3, 2009, at 9:45 AM, Peter wrote:

> ...
> Did you do this step?:
>>> Important!  If you are on a Windows platform, you need to put
>>> STDOUT into binary mode so that the PNG file does not go
>>> through Window's carriage return/linefeed transformations.
>>> Before the final print statement, put the statement
>>> binmode(STDOUT). This advice also applies to certain older
>>> versions of RedHat, which ship with a patched (and possibly
>>> broken) version of Perl.
>
> (BioPerl devs - couldn't that be added to the default
> render_blast1.pl script with an if statement checking for
> Windows?)
>
> Peter

Yes, that should be added.  I'll work on it.

chris
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Mauricio Herrera Cuadra | 3 Nov 18:20
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Re: svn errors?

Hi Aaron,

This was reported a few days ago. Chris Dagdigian is working today on a 
fix for it.

Mauricio.

Aaron Mackey wrote:
> [ajm6q <at> lc4 bioperl-live]$ svn update
> svn: Decompression of svndiff data failed
> 
> 
> I'll admit to not having svn updated in awhile; A clean, anonymous svn co
> failed with the same message:
> 
> [...]
> A    bioperl-live/Bio/Structure/StructureI.pm
> A    bioperl-live/Bio/Structure/IO
> svn: Decompression of svndiff data failed
> 
> -Aaron
> 
> P.S. I used this command: svn co svn://
> code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
(Continue reading)

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Rachita Sharma | 3 Nov 23:12
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Trouble parsing PSI-BLAST

I am having trouble parsing PSI-BLAST results. Please help.

The code is:
my $in = new Bio::SearchIO(        -format => 'blast',
                                -file =>
"BS_XFpsiRblastoutputs/e${ev}/bloutput${i}.txt");

while( my $result = $in->next_result ) {
while( my $hit = $result->next_hit ) {

$sth->execute($result->query_name, $hit->name, $hit->significance);
print "Query executed!\n";

}
}

The error is:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: no data for midline  ***** No hits found ******
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::SearchIO::blast::next_result
/usr/lib/perl5/site_perl/5.8.8/Bio/SearchIO/blast.pm:1813
STACK: BSubVCpsiRblast.pl:92
-----------------------------------------------------------
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Gmane