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Radwen Aniba | 1 May 2010 12:45
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Pfam_Scan

Hello everyone,

I would like to know if there is a way to cluster the output of Pfam_Scan
results.
I mean is we can parse it and then output clusters containing sequences
sharing the same domains or Pfams.
This is a bit special since we could have multidomains proteins inside,
which rule we have to follow in this case ?

Rad

--

-- 
R. ANIBA
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Dave Messina | 2 May 2010 00:28
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Re: Pfam_Scan

Hi Rad,

As far as I can tell the Pfam_Scan output is simply tab-delimited text (see details below), so you should be
able to group sequences which share domains by sorting on the sixth column. I suspect that sequences with
multiple domain hits will have multiple lines in the output, one per hit, so if you want to identify
sequences which share the same _set_ of domains you will have to do the bookkeeping yourself.

That being said, Pfam_Scan is not part of BioPerl — it's distributed by the Pfam team — so you may want to
contact them directly for help (pfam-help <at> sanger.ac.uk).

Dave

[from the Pfam_Scan documentation]
The output format is:
<seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type>
<hmm start> <hmm end> <hmm length> <bit score> <E-value> <significance> <clan> <predicted_active_site_residues>

Example output (with -pfamB, -as options):

  Q5NEL3.1      2    224      2    227 PB013481  Pfam-B_13481      Pfam-B     1   184   226    358.5  1.4e-107  NA NA
  O65039.1     38     93     38     93 PF08246   Inhibitor_I29     Domain     1    58    58     45.9   2.8e-12   1 No_clan
  O65039.1    126    342    126    342 PF00112   Peptidase_C1      Domain     1   216   216    296.0   1.1e-88   1 CL0125   predicted_active_site[150,285,307]
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Dave Messina | 2 May 2010 10:54
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Re: RFC: SNP::Inherit

Hi Christopher,

Looks good!

The only recommendation I would make is to change the namespace to Bio::SNP::Inherit.

The convention on CPAN is to minimize the number of new toplevel namespaces (which SNP would be), and
although many of the Bio::* modules are part of BioPerl, that namespace is not restricted to BioPerl and
there are plenty of non-BioPerl packages there.

Dave

On Apr 29, 2010, at 10:26 PM, Christopher Bottoms wrote:

> Dear Bioperl community,
> 
> I was thinking of uploading a module to CPAN that converts SNP genotype data
> to parental allele designations. Below is the perldoc. This is not a
> "BioPerl" module per se, so I'm  not sure what namespace to put it under.
> 
> I would be glad to send anyone the source if they are interested in checking
> it out more. I just did not want to send everyone an unsolicited attachment.
> 
> Thank you for your time,
> Christopher Bottoms (molecules)
>
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Dave Messina | 2 May 2010 11:59
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Re: question about Bio::Tools::Run::Genewise

Hi Dimitar,

The syntax you want is:

# Build a Genewise alignment factory
my $factory = Bio::Tools::Run::Genewise->new();

# turn on the quiet switch
$factory->QUIET(1);

#  <at> genes is an array of Bio::SeqFeature::Gene::GeneStructure objects
my  <at> genes = $factory->run($protein_seq, $genomic_seq);

This turns out be incorrectly documented on the man page, at least in part:
> Available Params:
> 
> NB: These should be passed without the '-' or they will be ignored,
> except switches such as 'hmmer' (which have no corresponding value)
> which should be set on the factory object using the AUTOLOADed methods
> of the same name.
> 
>   Model    [-codon,-gene,-cfreq,-splice,-subs,-indel,-intron,-null]
>   Alg      [-kbyte,-alg]
>   HMM      [-hmmer]
>   Output   [-gff,-gener,-alb,-pal,-block,-divide]
>   Standard [-help,-version,-silent,-quiet,-errorlog]

That is, these don't work as expected:

	$factory->quiet;
(Continue reading)

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Mark A. Jensen | 2 May 2010 21:28
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new core developers Rob Buels and Dave Messina

Hi Folks, 
On behalf of the core team, I am delighted to announce two new members: Rob Buels and Dave Messina. They are
so, er, honored on the basis of their selfless work on the list, on IRC, in development of new modules and
their active and sustained participation in BioPerl maintenance, design and promotion. 
Welcome Rob and Dave!
MAJ and the BioPerl core developers
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Lakshmi Kastury | 3 May 2010 04:41

Using BIO::SEARCHIO


I am attempting to use the BIO::SEARCHIO system to parse a Blast output file. 

A new instance is he file is read through the following:
my $input = new BIO::SearchIO (-file =>'blast_report_0.txt', -format =>'blast');

When I run my program, I receive the following message:
"Can't locate object method "new" via package "BIO::SearchIO" (perhaps you forgot to load "BIO::SearchIO"?

Is this an optional module which needs to be installed separately?

Thanks,
Lakshmi Kastury
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Mark A. Jensen | 3 May 2010 04:57
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Re: Using BIO::SEARCHIO

you need to say "Bio::SearchIO", and not "BIO::SearchIO"
MAJ
----- Original Message ----- 
From: "Lakshmi Kastury" <skastu01 <at> students.poly.edu>
To: <bioperl-l <at> lists.open-bio.org>
Sent: Sunday, May 02, 2010 10:41 PM
Subject: [Bioperl-l] Using BIO::SEARCHIO

>
>
>
>
>
>
>
>
>
>
>
> I am attempting to use the BIO::SEARCHIO system to parse a Blast output file.
>
> A new instance is he file is read through the following:
> my $input = new BIO::SearchIO (-file =>'blast_report_0.txt', -format 
> =>'blast');
>
> When I run my program, I receive the following message:
> "Can't locate object method "new" via package "BIO::SearchIO" (perhaps you 
> forgot to load "BIO::SearchIO"?
>
> Is this an optional module which needs to be installed separately?
(Continue reading)

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Chris Fields | 3 May 2010 06:22
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Full bioperl-live github demo

All, 

I have pushed a demo of the bioperl-live (all branches and tags) to github here:

http://github.com/bioperl/bioperl-test

This is separate from the 'bioperl-live' repo at the same github account for the time being.  The conversion
was performed using svn2git (the gitorious C++/Qt version from the KDE project migration, Jonathan
Leto's suggestion), using the rsync'ed svn repo via ssh from dev.open-bio.org, so an update and rerun can
be performed very quickly.  The actual conversion of the entire bioperl repo took very little time,
actually (less than 3 minutes).  I think, with some additional small work using the svn2git rules pretty
much everything is ready for migration.  

In this run, all subversion tags are converted to git tags (branches remain git branches as expected).  Just
in case I'm missing something, I would like everyone to take a look at this, though.  In particular, I would
like to make sure tags and branches are as they are expected.  So far I haven't seen anything that stands out
as odd.

chris
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Heikki Lehvaslaiho | 3 May 2010 13:45
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BLAST parsing broken

Chris,

latest additions to Bio::SearchIO::blast.pm broke the parsing of normal
blast output.  $result->query_name returns now undef.

(Using the anonymous git now). This change still works:

commit 5e278f5dbb9afc4dc0359cd3fdc8fb0d0f4cad74
Author: cjfields <cjfields <at> eb9725d8-4842-0410-9bbb-c0b52e2da49b>
Date:   Sun Dec 20 04:39:58 2009 +0000

    Robson's patch for buggy blastpgp output

But this does not:

commit 9a89c3434597104dd50553e3562983d78d14a544
Author: cjfields <cjfields <at> eb9725d8-4842-0410-9bbb-c0b52e2da49b>
Date:   Thu Apr 15 04:21:17 2010 +0000

    [bug 3031]

    patches for catching algorithm ref, courtesy Razi Khaja.

That makes it easy to find the diffs:

$git diff 5e278f5dbb9afc4dc0359cd3fdc8fb0d0f4cad74
9a89c3434597104dd50553e3562983d78d14a544   Bio/SearchIO/blast.pm
diff --git a/Bio/SearchIO/blast.pm b/Bio/SearchIO/blast.pm
index 378023a..6f7eeeb 100644
--- a/Bio/SearchIO/blast.pm
(Continue reading)

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Chris Fields | 3 May 2010 14:08
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Re: BLAST parsing broken

Odd, I ran tests on that prior to commit.  I'll work on fixing that (in svn of course, until the migration is complete).

chris

On May 3, 2010, at 6:45 AM, Heikki Lehvaslaiho wrote:

> Chris,
> 
> latest additions to Bio::SearchIO::blast.pm broke the parsing of normal
> blast output.  $result->query_name returns now undef.
> 
> (Using the anonymous git now). This change still works:
> 
> commit 5e278f5dbb9afc4dc0359cd3fdc8fb0d0f4cad74
> Author: cjfields <cjfields <at> eb9725d8-4842-0410-9bbb-c0b52e2da49b>
> Date:   Sun Dec 20 04:39:58 2009 +0000
> 
>    Robson's patch for buggy blastpgp output
> 
> But this does not:
> 
> commit 9a89c3434597104dd50553e3562983d78d14a544
> Author: cjfields <cjfields <at> eb9725d8-4842-0410-9bbb-c0b52e2da49b>
> Date:   Thu Apr 15 04:21:17 2010 +0000
> 
>    [bug 3031]
> 
>    patches for catching algorithm ref, courtesy Razi Khaja.
> 
> That makes it easy to find the diffs:
(Continue reading)

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Gmane