Mlagan/lagan bioperl object

Hi-

I figured out that SimpleAlign takes the multi-alignments.  Just warns 
you and overwrites if they have the same name.
Bio::Tools::Lagan is attached and some hacked up test script for those 
wanting to give it a try in their bioperl distro.
If it is integrated, I'll CVS in further updates (thinking... damn I 
wonder how many people are getting a module they care nothing about in 
their mailbox? :) ).  
Have a good weekend all.

Cheers,
Stephen

-----------------------------
Stephen Montgomery
Genome Sciences Centre
Vancouver, BC Canada
-----------------------------

#!/usr/bin/perl

##Slammed together by Stephen Montgomery (Genome Sciences Centre, Vancouver)
##January 31st, 2003 
##A test driver for the Lagan bioperl object
##Copyright Bioperl

use strict;
use Bio::Tools::Lagan;

Re: Mlagan/lagan bioperl object

Committed to Bioperl -

Stephen - could you contribute a test script as well (check out
bioperl-live/t) to test it.

We'll give a cvs a/c pretty soon so you can maintain it...

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney <at> ebi.ac.uk>. 
-----------------------------------------------------------------

Parsing GenBank files w/o Sequences

Hi,

I'm new to Bioperl (wrote my first script two days ago), so I may be
trying to do something the wrong way.  I want to read GenBank files that
have all of the sequence features annotated, but don't actually have any
sequence, e.g. files like
ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/H_sapiens/CHR_22/hs_chr22.gbs.gz

Thanks to the wiki pages, I quickly hit on Bio::SeqIO and the sample
code to read GenBank records.  Unfortunately, when there are multiple
entries in a GenBank file, but no sequence for the records (no ORIGIN
section), the parser skips over every other entry without any kind of
warning message.

Am I correct in thinking that Bio::SeqIO;;genbank should handle this
type of GenBank record?  If so, I have a patch and some new tests to
contribute--I'll send them to Elia unless someone else wants them.  If
Bio::SeqIO;;genbank is not the best way to deal with these, please point
me toward the correct modules to use, and perhaps I'll look for a good
place to document this.

Thanks,
Peter

RE: Errors using Bio::Assembly

Thanks for the quick response, I will be at the OReilly conference next 
week so no rush.  I would add the bit about the qual files in the docs.  I 
was wondering how you were calling high qual discrenpancies, and i thought 
it was just the default upper/lower case you were using in the trace 
sequences in the ace file.  Also, the high_quality_discrepancies returns 
an array of Bio::SeqFeatures::Generic objects yes? but in the web 
documentation it says a SeqFeature Collection object.

My ace files are not in the context of phredphrap. I only save the ace 
files themselves.  I think I will attempt to right a method that will do 
high qual discrepancies based on the ace file itself.

Thanks again, this does help alot
Andy
 On Fri, 31 Jan 2003, 
Robson Francisco de Souza wrote:

> 
> 	Hi Andy,
> 
> 	You are trying to use a Bio::Assembly::Contig method that depends
> on quality values for the read sequences, but you haven't the appropriate
> quality objects first. An ACE file has no data about read base qualities,
> those are loaded by consed from the phd file in ../phd_dir. To use
> high_quality_discrepancies from Bio::Assembly::ContigAnalysis, you must
> first add quality objects using set_seq_qual. See my changes to you code
> below. See my comments on the other errors after the code.
> 
> use lib '/loginhome/anunberg/bioperl-1.2';
> use strict;

RE: Errors using Bio::Assembly

On Sat, 1 Feb 2003 anunberg <at> oriongenomics.com wrote:
[snip]
>  Also, the high_quality_discrepancies returns 
> an array of Bio::SeqFeatures::Generic objects yes? but in the web 
> documentation it says a SeqFeature Collection object.

	Yes, the documentation is incorrect. All methods in
Bio::Assembly::ContigAnalysis return arrays, not collections. I'll fix
that. 

> My ace files are not in the context of phredphrap. I only save the ace 
> files themselves.  I think I will attempt to right a method that will do 
> high qual discrepancies based on the ace file itself.

	Which program builds your ace files? Phrap, CAP3? Maybe I can add
support for it...

				Robson

Re: problem with Bio::DB::Query::GenBank

True. Believe it or not, but I don't even know much about how to do 
tagged exports in perl ... maybe it's time to learn. Aaron, do you know 
how to do this or do I have to dig?

	-hilmar

On Friday, January 31, 2003, at 01:26  PM, Ewan Birney wrote:

>
>
> On Fri, 31 Jan 2003, Hilmar Lapp wrote:
>
>> Aaron I like this. Sounds sane, and would make things very simple for
>> the user.
>
> You both have cvs commit priviledges - go for it ;) (I suggest main 
> trunk
> only)
>
>
>
>
--

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

Re: Parsing GenBank files w/o Sequences

Probably genbank.pm should handle this. There is code in DB::GenBank  
redirecting to DB::RefSeq on certain accessions (CONTIGs I believe),  
but that's probably not applicable here.

Can you send me your patch?

	-hilmar

On Saturday, February 1, 2003, at 08:42  AM, Peter Chines wrote:

> Hi,
>
> I'm new to Bioperl (wrote my first script two days ago), so I may be
> trying to do something the wrong way.  I want to read GenBank files  
> that
> have all of the sequence features annotated, but don't actually have  
> any
> sequence, e.g. files like
> ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/H_sapiens/CHR_22/ 
> hs_chr22.gbs.gz
>
> Thanks to the wiki pages, I quickly hit on Bio::SeqIO and the sample
> code to read GenBank records.  Unfortunately, when there are multiple
> entries in a GenBank file, but no sequence for the records (no ORIGIN
> section), the parser skips over every other entry without any kind of
> warning message.
>
> Am I correct in thinking that Bio::SeqIO;;genbank should handle this
> type of GenBank record?  If so, I have a patch and some new tests to
> contribute--I'll send them to Elia unless someone else wants them.  If

Re: gene ontology

I guess it depends a lot on what provides you with the associations. Do 
you want to start from LocusLink? Or with one of the association tables 
provides by (I think) GO, Swissprot, NCBI, or Ensembl?

	-hilmar

On Friday, January 31, 2003, at 05:46  AM, Ingrid Marchal wrote:

> Hi,
>
> I would like to make a bioperl script to retrieve all the gene 
> products associated with a given GO term, but I can't figure out where 
> to start....
> Thank you for your help !
> Ingrid
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
--

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

Re: Mlagan/lagan bioperl object

Cool, very useful, as we are just looking to do some work with it.
Just a note Ewan, should we instead add this to the Bio::Tools::Run:: name space under bioperl-run
as it is a wrapper more than a parser? I can volunteer to integrate this.

cheers,

shawn

On Fri, 31 Jan 2003, Stephen Montgomery wrote:

> Hi-
> 
> I figured out that SimpleAlign takes the multi-alignments.  Just warns 
> you and overwrites if they have the same name.
> Bio::Tools::Lagan is attached and some hacked up test script for those 
> wanting to give it a try in their bioperl distro.
> If it is integrated, I'll CVS in further updates (thinking... damn I 
> wonder how many people are getting a module they care nothing about in 
> their mailbox? :) ).  
> Have a good weekend all.
> 
> Cheers,
> Stephen
> 
> -----------------------------
> Stephen Montgomery
> Genome Sciences Centre
> Vancouver, BC Canada
> -----------------------------
> 

StandAlone BLAST error

Hi

I am trying to blast sequences from a COG against a single sequence in a loop. After successfully blasting
about 10 sequences, I get the following error. Can anybody throw some light on this ? Thanks in advance for
any comments.

Arvind

------------- EXCEPTION  -------------
MSG:  No hit object found for bl2seq report
STACK Bio::Tools::BPbl2seq::next_feature C:/Perl/site/lib/Bio/Tools/BPbl2seq.pm:
239
STACK toplevel hw3.pl:83
--------------------------------------
Error removing C:\windows\TEMP\Jiu9H1ueKt at C:/Perl/lib/File/Temp.pm line 839,
<GEN26> line 36.
The offending code looks something like
...

my  <at> params = ('program' => 'blastp');
my $factory = Bio::Tools::Run::StandAloneBlast->new( <at> params);
my $evalue = 0.0001;
$factory->e($evalue);

...
      $cogIO = Bio::SeqIO->new(-file => $cogfile, -format => 'fasta');
      # for every sequence in the cog file, blast against $myseq
      while ($seq = $cogIO->next_seq()) {
        if ($report = $factory->bl2seq($seq, $myseq)) {
         if ($hsp = $report->next_feature) {