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Brian Osborne | 1 Jan 2005 17:18

RE: Bioperl in 2005

Ryan,

You could post it to bioperl-l, some one will commit it to CVS.

Brian O.

-----Original Message-----
From: bioperl-l-bounces <at> portal.open-bio.org
[mailto:bioperl-l-bounces <at> portal.open-bio.org]On Behalf Of Ryan Golhar
Sent: Thursday, December 30, 2004 12:33 PM
To: 'Jason Stajich'; 'Bioperl List'
Subject: RE: [Bioperl-l] Bioperl in 2005

Hi all,

I'd like to contribute a parser module to parse Spidey results.  I took
the sim4 parser and modified a little bit to properly read in spidey
results.  Everything else about it works the same as the sim4 parser as
far as I can tell.

How can I contribute this module?

-----
Ryan Golhar
Computational Biologist
The Informatics Institute at
The University of Medicine & Dentistry of NJ

Phone: 973-972-5034
Fax: 973-972-7412
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James Thompson | 1 Jan 2005 08:32

Re: Re: Questions about Bio::AlignIO::maf

Alison,

You're right on this, I just committed the fix to maf.pm. This also fixed
a range problem in the AlignIO.t test script and the associated humor.maf
test data file, I just committed fixes for those as well.

Thanks for the fix. :)

Cheers,

James Thompson

On Thu, 30 Dec 2004, Lee Ping Alison wrote:

> Hi Mr Thompson,
> 
> Thanks for the reply. I understand the need for the one-based inclusive
> coordinate system now; also partly because the major genome browsers use
> that. However, since you're using inclusive coords, then shouldn't you add 1
> to $start first before calculating $end, since $start is zero-based?
> 
> Alison.
> 
> ----- Original Message -----
> From: "James Thompson" <tex <at> biocompute.net>
> To: "Lee Ping Alison" <g0404203 <at> nus.edu.sg>
> Cc: "Allen Day" <allenday <at> ucla.edu>; "Bioperl" <bioperl-l <at> bioperl.org>
> Sent: Wednesday, December 29, 2004 3:30 PM
> Subject: Re: [Bioperl-l] Re: Questions about Bio::AlignIO::maf
>
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rj144331 | 2 Jan 2005 23:56
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Extract sequences from .msf

Hi,
I am a second year graduate student in Baylor College of Medicine, Houston, TX 
majoring in bioinformatics. I would like to know how to extract protein 
sequences and store them in fasta format from a html page containing the 
multiple sequence alignment using perl. Any help would be appreciated.

Thanks,
regards,
Rupashree Jayashankar
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Hilmar Lapp | 3 Jan 2005 01:28
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score in seqfeature

Allen et al, what are the (GFF3-driven?) plans for storing the score 
property introduced by SeqFeature::Generic?

The reason I'm asking is that it doesn't get (de-)serialized in 
bioperl-db because it's neither defined on SeqFeatureI nor has it been 
internal stored as a tag/value pair. I'd like to fix this issue, either 
by pulling it into the annotation bundle in 
SeqFeature::AnnotationAdapter, or by some other means that maybe is 
friendlier or more useful to GFF3 minds.

	-hilmar
--

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------
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Rasa Gulbinaite | 3 Jan 2005 15:41

Fasta headers

Hello,

i'm new to bioperl and a bit confused with fasta file headers. I'm working
with SNPs and i would like to get only the fasta headers form the fasta
file, not the sequences. What would be the best way to do this? Thank you.

Rasa
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Venky Nandagopal | 3 Jan 2005 15:23
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Bio::DB::Fasta errors

I've been noticing some errors with Bio::DB::Fasta indices. Working with  
different assemblies of a genome, I've been creating symlinks latest/ to  
the latest assembly directory, and genome.fasta to the latest assembly  
fasta file. When I pass latest/genome.fasta to Bio::DB::Fasta, I get a  
genome.fasta.index file, and retrieval works in my script. But then when I  
run a different analysis on it,  or access the same file after a while, I  
get undef for sequences I know for sure to be in the database. Reindexing  
will fix the problem. I'm not certain if this is simply due to the  
symlinks, or a more general issue with Bio::DB::Fasta. Does anyone have  
suggestions?

Venky

--

-- 
___
Venky Nandagopal
Graduate Student
Eisen Lab
UC Berkeley
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Ewan Birney | 3 Jan 2005 15:59
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Picon
Favicon

Re: Fasta headers


On Mon, 3 Jan 2005, Rasa Gulbinaite wrote:

> Hello,
>
> i'm new to bioperl and a bit confused with fasta file headers. I'm working
> with SNPs and i would like to get only the fasta headers form the fasta
> file, not the sequences. What would be the best way to do this? Thank you.

The desc() method on a sequence object has this - eg:

$seqin = Bio::SeqIO->new( -file => 'my_filename' , -format => 'fasta');

while( ($seq = $seqin->next_seq()) ) {
   $header = $seq->desc();
}

>
> Rasa
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
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Sean Davis | 3 Jan 2005 16:27
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Re: Fasta headers

Rasa,

You can parse the fasta file with seqio, but if you only want the headers 
"as-is", something like this from the command line might do:

cat fastafile.fa > perl -e 'while (<>) {print "$_\n" if ($_ =~ /^>/)}'

Sorry, I didn't test this....

Sean

----- Original Message ----- 
From: "Rasa Gulbinaite" <rasa <at> obj.hopto.org>
To: <bioperl-l <at> portal.open-bio.org>
Sent: Monday, January 03, 2005 9:41 AM
Subject: [Bioperl-l] Fasta headers

> Hello,
>
> i'm new to bioperl and a bit confused with fasta file headers. I'm working
> with SNPs and i would like to get only the fasta headers form the fasta
> file, not the sequences. What would be the best way to do this? Thank you.
>
> Rasa
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
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Guillaume Rousse | 3 Jan 2005 16:53
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Need help for implementing a new TreeIO module

I'm trying to implement a Bio::TreeIO module for parsing 
Alogrithm::Cluster::treecluster output, and I need some help about the 
tree event builder module. Reading the code, I understand I can add 
elements of type 'tree', 'branch-length', 'id', 'node', and 'leaf', and 
also add characters. However, I don't really understand how it works...

Basically, I know all leaves right from given parameters. Then I parse a 
result table, line by line, each new line being an internal node whose 
length is given. So I guess, the code should be similar to:

$self->_eventHandler->start_document;
$self->_eventHandler->start_element( {'Name' => 'tree'} );

# leaves
foreach my $label ( <at> {$self->{_labels}} {
     $self->_eventHandler->start_element( {'Name' => 'leaf'} );
     $self->_eventHandler->characters($label);
     $self->_eventHandler->end_element( {'Name' => 'leaf'} );
}

# nodes
foreach my $line ( <at> {$self->{_result}} {
     $self->_eventHandler->start_element( {'Name' => 'node'} );
     # this node result from the merge of two already existing leaves or 
nodes with a known distance
     $self->_eventHandler->end_element( {'Name' => 'node'} );
}

$self->_eventHandler->end_element( {'Name' => 'tree'} );
my $tree = $self->_eventHandler->end_document;
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Guillaume Rousse | 3 Jan 2005 16:59
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Re: Installing bioperl-ext-1.4

bcur001 <at> ec.auckland.ac.nz wrote:
> I am wanting to run code to do smith-waterman alignment. From what I can see, I
> need the EMBOSS suite, which appears to come as part of bioperl-ext-1.4.
> 
> I have installed bioperl-1.4 fine. when I attempt to install bioperl-ext-1.4
> however, I encounter problems. I've worked my way through a few initial errors,
> finding and installing the staden library and the Inline pm (both of which
> appear to ahve installed fine), I have, however, finally been stumped. Upon
> attempting to run `perl Makefile.PL` from the bioperl-ext-1.4/ directory, I get
> the following:
> 
> Writing Makefile for Bio::Ext::Align
> Found Staden io_lib "libread" in /usr/local/lib ...
> Automatically using the Read.h found in /usr/local/include/io_lib ...
> Writing Makefile for Bio::SeqIO::staden::read
> Writing Makefile for Bio
> One or more DATA sections were not processed by Inline.
Sorry, I missed this post.

Unless you have really good reasons to do so, you'd better use official 
contrib packages for EMBOSS, io_lib and bioperl (I'm the maintainer) 
instead of attempting manual installs. EMBOSS is installed with better 
defaults as by default installation script, io_lib is patched for wrong 
headers, and Bioperl has every needed dependencies packaged. Only 
bioperl-ext is missing, because I never succedeed building it due to 
problem in Makemaker::Inline.

Just try:
urpmi emboss perl-Bioperl-Run libio_lib1-devel
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Gmane