Thiago M. Venancio | 17 Dec 19:04 2014
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MSG: Undefined sub-sequence

Hi all,
I am parsing a BLASTX report and got the following error for some sequences.
It always happen with sub-sequences of 1 base. I found some posts on this issue, but they are old.
I am use the latest version installed through cpan.
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
1.006924

Any help is appreciated.
Thiago

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Undefined sub-sequence (241,242). Valid range = 96 - 242
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Search::HSP::HSPI::matches /usr/share/perl5/Bio/Search/HSP/HSPI.pm:716
STACK: Bio::Search::SearchUtils::_adjust_contigs /usr/share/perl5/Bio/Search/SearchUtils.pm:431
STACK: Bio::Search::SearchUtils::tile_hsps /usr/share/perl5/Bio/Search/SearchUtils.pm:201
STACK: Bio::Search::Hit::GenericHit::frac_aligned_hit /usr/share/perl5/Bio/Search/Hit/GenericHit.pm:1319

--
=================================
Thiago Motta Venancio, M.Sc., PhD
http://venancio.openwetware.org/
=================================
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Thiago Venancio | 17 Dec 18:14 2014
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MSG:

Hi all,
I am parsing a BLASTX report and got the following error for some sequences.
It always happen with sub-sequences of 1 base. I found some posts on this issue, but they are old.
I am use the lates version installed through apt-get.
Any help is appreciated.
Thiago

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Undefined sub-sequence (241,242). Valid range = 96 - 242
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Search::HSP::HSPI::matches /usr/share/perl5/Bio/Search/HSP/HSPI.pm:716
STACK: Bio::Search::SearchUtils::_adjust_contigs /usr/share/perl5/Bio/Search/SearchUtils.pm:431
STACK: Bio::Search::SearchUtils::tile_hsps /usr/share/perl5/Bio/Search/SearchUtils.pm:201
STACK: Bio::Search::Hit::GenericHit::frac_aligned_hit /usr/share/perl5/Bio/Search/Hit/GenericHit.pm:1319

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Hannes Hettling | 17 Dec 12:17 2014
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RaXML wrapper

Dear bioperl developers,

some weeks ago I noticed that using Bio::Tools::Run::Phylo::Raxml, RaXML’s ‘-w’ option was not
working and the unit tests also failed.
I made an attempt to fix this, adjusted the tests and send a pull request on Github. Since I have not heard
anything for a month now I wanted to ask
whether the changes can be considered. What is the preferred way to communicate about such matters (maybe
other than pull requests)?

Thanks,

Hannes
Weigang Qiu | 9 Dec 22:01 2014
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Bb-utils

Dear BioPerl developers,

I intend to share & (eventually) publish a suite of bioperl-based command-line utilities my lab has developed & found very useful in the past 10 years:

http://diverge.hunter.cuny.edu/labwiki/Bioutils

Hilmar encouraged me to get some feedback & advice from the bioperl-L on how to package and release it properly.

My specific questions are:

1. While it goes naturally with bioperl releases, but I would like it to be more exposed than hidden inside the bp-scripts folder. Do you think these utilities are useful enough to be housed in a separate folder (e.g., "bputils") by itself? I have a developer's account but I haven't commit anything for years.

2. How to make it sustainable (and attract new developers) since we are constantly revising and adding methods. It would be great if become a part of bioperl-live.

Any advice and facilitation will be appreciated!

Thanks,
--
Weigang Qiu, Ph.D.
Department of Biological Sciences
Hunter College of the City University of New York
695 Park Avenue, New York, NY 10065
Office: 1-212-772-5296 (Room 839 Hunter North Building)
Lab: 1-212-772-5721 (Room 830 Hunter North Building)
Web:http://diverge.hunter.cuny.edu/labwiki/

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newtoperlprog | 24 Nov 23:07 2014
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parse genebank for gene name/ id

Dear All,

I am trying to parse a genebank summary files for the following records:

Sequence, description, division, GI number, gene id/name, version and organism.

I used a script from the bioperl webpage and used to parse the above.

I am getting problem parsing the gene id/name, version and cds information, organism.

Could you please help with the same.

Below is the code I am using:

 #!/usr/bin/perl                                                                                                                                                                       
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Seq;

my $seqobj;
my $file = "NM_000040.summary";

my $seqio = Bio::SeqIO->new (-format => 'GenBank',
                             -file   => $file);
print ref($seqio);
while ($seqobj = $seqio->next_seq ()) {
    printf "Sequence:    %s\n",$seqobj->seq;
    printf "Display ID:  %s\n",$seqobj->display_id;
    printf "Description: %s\n",$seqobj->desc;
    printf "Division:    %s\n",$seqobj->division;
    printf "Accession:   %s\n",$seqobj->accession_number;
    printf "GI number:   %s\n",$seqobj->primary_id;
    printf "Definition:  %s\n",$seqobj->seq_version;
}

Any help is greatly appreciated.
Regards



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Jennifer Krauel | 20 Nov 19:45 2014
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Re: Error dereferencing sequence in SeqIO object

Well.  I made a very small fastq input file, stripped out all possible code, ran it in the debugger, and then it started working.  Now the original code and data files also work.  File it under "just keep trying stuff".

On Wednesday, November 12, 2014 6:01:01 PM UTC-6, Jennifer Krauel wrote:
I'm having some trouble running a very basic bioperl script to transform a fastq file into a fasta file.  When I try to dereference a sequence object I get this error: "Can't call method "seq" without a package or object reference..."
It's boilerplate code, and the error is on the last line in the snippet below:

my $seq_in = Bio::SeqIO->new(
                             -file   => "<$infile",
                             -format => $infileformat,
                             );
my $i=0;
while (my $this_seq = $seq_in->next_seq && $i < 100)
    { #while more sequences in fastq file
   
    $i++;
    my $seqstring = $this_seq->seq();
...

The counter is just to limit the number of reads while I'm testing the code, I don't think it should be causing the problem. I tried to google the error but didn't come up with anything useful except the suggestion that I might not be working with a clean or up to date bio perl installation.

When I try to get the bioperl version using this code:
perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
I get 1.005002102, which seems odd.

When I ask for the version number of SeqIO using
perl -MBio::SeqIO -e 'printf "%vd\n", $Bio::SeqIO::VERSION'
I get 49.46.48.48.53.48.48.50.49.48.50.

I am using CloudBioLinux on AWS, with whatever standard installation that provides (which is the whole point of using AWS).

Is there something bone-headed I am doing, or is this an issue I should pursue with the Cloud folks?

Thanks!
Jennifer

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Fields, Christopher J | 17 Nov 16:50 2014

Next bioperl release

I will likely start working on a new BioPerl release in the next week or two to attempt fixing some of the CPAN
indexing problems that have plagued us in the last few releases (final version to be mentioned when that is
fixed :).  

Along those lines, a few things when committing code:

1) Add yourself to the AUTHORS file if you have ben making code changes.  We like to give credit where credit is due!
2) Please make sure to update the ‘Changes’ file if appropriate.  This is particularly important if the
changes are addressing bugs or adding functionality.
3) Make sure anything potentially code-breaking is made on a branch first and merged in.  This hasn’t been
a problem recently (the coveralls work that Franscisco is unfortunately easier to deal with on master, so
that is a clear exception).

Thanks!

chris
Doug Hershberger | 14 Nov 00:04 2014
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Looking for recommendations for a Perl web security consultant

Our company is beefing up our overall computer security. This includes making modifications to many custom legacy web based Perl cgi bioinformatics databases, as well as refactoring a few of these applications using the Perl Catalyst framework. We are looking for a consultant with expertise in Perl web security, preferably someone who also has experience with Catalyst best practices to review our code and make recommendations and/or rewrite some necessary pieces.  If they possess any relevant web application security credentials, that would be a plus.

Thanks in advance for any help you can provide in our search.
--
Doug Hershberger
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Cacau Centurion | 10 Oct 19:46 2014
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Problems when using PAML::yn00

Hi All,

I tried to use PAML:Yn00 to run yn00 and parse the result. However, no results were given. Does anyone know what might be the problem?

The following code is obtained from 

use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(
    -format => 'fasta',
    -file   => "$ARGV[0]"
);
my $aln = $alignio->next_aln;

my $yn = Bio::Tools::Run::Phylo::PAML::Yn00->new();
$yn->alignment($aln);
my ( $rc, $parser ) = $yn->run;
while ( my $result = $parser->next_result ) { 
    my <at> otus     = $result->get_seqs();
    my $MLmatrix = $result->get_MLmatrix();

    #0 and 1 correspond to the 1st and 2nd entry in the <at> otus array
    my $dN   = $MLmatrix->[0]->[1]->{dN};
    my $dS   = $MLmatrix->[0]->[1]->{dS};
    my $kaks = $MLmatrix->[0]->[1]->{omega};
    print "Ka = $dN Ks = $dS Ka/Ks = $kaks\n";
}


###########################################################
Alignment:
>1
aaattgttgttg
>2
aacaatttgttg


Yours,
Cacau
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Andreas Prlic | 7 Oct 20:52 2014
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The NIH Software Discovery Index | We invite your comments -- a system for linking software, publications and users in the research community.

Greetings Everyone,

 

On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported meeting that focused on the opportunities and challenges of developing a software management ecosystem that could be valuable for finding and linking software, publications and users in the research community. You may be also be aware of a related project, the Data Discovery Index, which will be fully integrated with the software system.

The product of this workshop and the subsequent discussion is a document which details the opportunities and challenges of developing a Software Discovery Index that would enable researchers to find, cite, and link software and analysis tools publications and researchers. To ensure that the opportunities, challenges, and recommendations detailed in the document reflect the breadth of experience from the community, we are seeking your input.  In conjunction with related efforts already under way at NIH, including the development of a Data Discovery Index, the final document will be used by the NIH Office of the Associate Director (ADDS) to inform a strategy for the development of a Software Discovery Index and a commons ecosystem for data, software, and resources.

 

We need your help to ensure that this critical task is achieved: to guide the development of a community based system that gives credit and acknowledgment to the builder and maintainers of the software we all depend on! We invite all users, software developers, publishers, and software repository administrators to review our report prior to its submission to the NIH. Please complete your review and post comments by November 1, 2014.

 

The link to the report is here: http://softwarediscoveryindex.org

 

On behalf of the organizing committee, thank you for your assistance!

 

Organizing Committee

 

Owen White

Director of Bioinformatics, University of Maryland, Baltimore, School of Medicine

Co-Chair of NIH BD2K  Software Index Workshop

 

Asif Dhar

Principal & Chief Medical Informatics Officer

Co-Chair of NIH BD2K  Software Index Workshop

 

Vivien Bonazzi

Senior Advisor for Data Science Technologies (ADDS)

Co-Chair of BD2K Software and Methods Group

 

Jennifer Couch

Chief, Structural Biology and Molecular Applications Branch

NCI Co-Chair of BD2K Software and Methods Group

 

Chris Wellington

Program Director (NHGRI)

 

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Alexey Morozov | 30 Sep 08:20 2014
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Getting pairwise alignment scores for existing multiple alignment

Dear colleagues,
Is there a method in bioperl that will calculate pairwise alignment scores for any given pair of genes in MSA (according to a given matrix and gap opening/extension cost)? It seems that Bio::SimpleAlign methods only work with score if it has been described in MSA file and can only hold a general multiple sequence alignment score.

--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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Gmane