Wilson, Colin (CC | 4 Mar 01:13 2015
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Bio:Seq->translate with orf=1; behavior change between 1.5 and 1.6

I've got an older application that I'm migrating from BioPerl 1.5 to 1.6.923, and it didn't pass testing due
to a change in the behavior of Bio:Seq::translate between 1.5 and 1.6

Per  the bioperl documentation Seq->translate(-orf=> 1) should return the first orf in a sequence.   It
appears to be returning the orf upstream of the first stop codon, so an internal out of frame orf is found
instead of a full length orf.

Here's my test code.   It passes in 1.5, fails in 1.6.  Is there a switch or different parameter to get the old
behavior?  Is this a bug or intentional change in translate?  
------------
use strict;
use Bio::Seq;

my ($bs, $prot, $orf0, $orf1, $orf) ;
$bs = Bio::Seq->new( -seq           => "ATGAATGTAAATAA",
		   -display_id       => "TestSequence",
		   -alphabet         => 'dna' );

$orf0 = $bs->translate(-frame=>0);
$orf1 = $bs->translate(-frame=>1);

# should output MNVN orf that starts in frame 0, not M* orf that starts in frame 1
$orf = $bs->translate(-orf=>1, -start=> 'atg');
if ($orf0->seq eq $orf->seq) {
        print "PASS";
}
else {
    print $orf0->seq . " != " . $orf->seq . "\n";
}
(Continue reading)

lawrence.benbow | 14 Mar 15:04 2015
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Bioperl/cygwin/ubuntu installation issues

Hello all,

I'm new to bioperl and I have tried with no success to install on both Windows 8/Cygwin and ubuntu(Mint). I hope that someone can point me in the right direction.

I have followed the instructions in the bioperl wiki. In both cases I tried using the CPAN method which had multiple dependency issues, then reverted to downloading and building the modules manually. I just kept getting more and more dependency errors until I finally gave up. Here's a list of the modules I had to install:

Algorithm-Diff-1.1903.tar.gz
BioPerl-1.6.924.tar.gz
Class-Data-Inheritable-0.08.tar.gz
CPAN-Meta-2.143240.tar.gz
CPAN-Meta-Requirements-2.133.tar.gz
CPAN-Meta-YAML-0.012.tar.gz
Data-Stag-0.14.tar.gz
Devel-StackTrace-2.00.tar.gz
Exception-Class-1.39.tar.gz
inc-latest-0.500.tar.gz
IO-String-1.08.tar.gz
JSON-PP-2.27300.tar.gz
Module-Build-0.4211.tar.gz
Parse-CPAN-Meta-1.4414.tar.gz
Sub-Uplevel-0.25.tar.gz
Test-Deep-0.115.tar.gz
Test-Differences-0.63.tar.gz
Test-Exception-0.38.tar.gz
Test-Most-0.34 (1).tar.gz
Test-Most-0.34.tar.gz
Test-NoWarnings-1.04.tar.gz
Test-Simple-1.001014.tar.gz
Test-Warn-0.30.tar.gz
Text-Diff-1.41 (1).tar.gz
Text-Diff-1.41.tar.gz

Any ideas on what I may be doing wrong? I know it can't be this difficult!

Best, Larry
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Fields, Christopher J | 12 Mar 04:57 2015

[Bosc-announce] BOSC 2015 Call for Abstracts

Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015)
A Special Interest Group (SIG) of ISMB/ECCB 2015

Dates: 10-11 July, 2015
Location: Dublin, Ireland
Web site: http://www.open-bio.org/wiki/BOSC_2015
Email: bosc <at> open-bio.org
BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
March 24, 2015: Registration opens for ISMB and BOSC (https://www.iscb.org/ismb2015-registration)
April 3, 2015: Deadline for submitting BOSC abstracts
May 3, 2015: Notification of accepted talk abstracts emailed to authors
July 8-9, 2015: Codefest 2015, Dublin (http://www.open-bio.org/wiki/Codefest_2015)
July 10-11, 2015: BOSC 2015, Dublin (http://www.open-bio.org/wiki/BOSC_2015)
July 10-14, 2014: ISMB/ECCB 2015, Dublin

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. We particularly wish to invite those who have not participated in previous BOSCs to join us this year!

Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.

We invite you to submit one-page abstracts for talks and posters. As mentioned, any topics relevant to open source bioinformatics and open science are welcome. Here are some potential session topics (but please don't feel limited to these!):
  Open Science and Reproducible Research
  Standards and Interoperability
  Data Science
  Visualization
  Translational Bioinformatics
  Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in being a sponsor for BOSC 2015, please contact us! Sponsors in 2014 included Google, Eagle Genomics, GigaScience, and Curoverse--we thank them for their support.

BOSC 2014 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, and Monica Munoz-Torres.
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Fields, Christopher J | 8 Mar 18:01 2015

Re: Bug in Bio::Phenotype::OMIM::OMIMparser

Peng,

Please post questions to the main BioPerl list (cc'd), and bug reports to our github tracker:

https://github.com/bioperl/bioperl-live/issues

After the bug is submitted we'll have a look but realize this is an open source project, and our time is pretty
constrained.  In the meantime if you have time to dive in and make a suggested fix we'll be more than happy to
accept it (patches are welcome but github pull requests are even better).

Chris

Sent from my iPhone

> On Mar 8, 2015, at 12:21 AM, Peng Yu <pengyu.ut <at> gmail.com> wrote:
> 
> Hi Chris,
> 
> Bio::Phenotype::OMIM::OMIMparser can not process title with multiple
> lines correctly. See the following test case. Would you please fix it?
> Thanks.
> 
> ~$ cat main.pl
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> 
> use Bio::Phenotype::OMIM::OMIMparser;
> my $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new(
>  -omimtext => '/dev/stdin' #$ARGV[0]
> );
> 
> while(my $omim_entry = $omim_parser->next_phenotype()) {
>  print $omim_entry->title(), "\n";
> }
> ~$ cat main.sh
> #!/usr/bin/env bash
> 
> (
> echo '*RECORD*'
> echo '*FIELD* NO'
> echo '616192'
> echo '*FIELD* TI'
> echo '#616192 ATAXIA, COMBINED CEREBELLAR AND PERIPHERAL, WITH HEARING LOSS AND'
> echo 'DIABETES MELLITUS; ACPHD'
> ) | ./main.pl
> 
> ~/linux/test/perl/library/Bio/Phenotype/OMIM/OMIMparser/new/next_phenotype/title$
> ./main.sh
> #616192 ATAXIA, COMBINED CEREBELLAR AND PERIPHERAL, WITH HEARING LOSS AND
> 
> --
> Regards,
> Peng
Thiago Venancio | 27 Feb 21:47 2015
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MSG: Start/stop out of range | Bio::Search::Tiling::MapTiling

Hi all,

By running the following code in the BLAST report attached I get the following error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Start/stop out of range [824, 1141]
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.20.1/Bio/Root/Root.pm:449
STACK: Bio::Search::HSP::HSPI::matches_MT /usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTileUtils.pm:583
STACK: Bio::Search::Tiling::MapTiling::_calc_stats /usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:1163
STACK: Bio::Search::Tiling::MapTiling::length /usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:508
STACK: Bio::Search::Tiling::MapTiling::num_aligned /usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:694
STACK: Bio::Search::Tiling::MapTiling::frac_aligned /usr/local/share/perl/5.20.1/Bio/Search/Tiling/MapTiling.pm:668
STACK: blParse.pl:40
-----------------------------------------------------------

I used the following code:

use strict;
use warnings;
use Bio::SearchIO;
use Bio::Search::Tiling::MapTiling;

my $searchio = Bio::SearchIO->new( -format => 'blast',
  -file   => shift );

my $gene;

while ( my $result = $searchio->next_result() ) {

    $result->query_name =~ /(\S+_\S+)_i/;
    my $g = $1;

    while( my $hit = $result->next_hit ) {
        
my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
my $hsp    = $hit->next_hsp;

my $st    = $hsp->query->strand == "1" ? "p" : "m";
my $frame = $hsp->query->frame;
my $context = $st.$frame;

print $tiling->frac_aligned('query', 'exact', $context)."\n";
    }
}

Any clues on how to deal with this error ?

Thanks in advance.
Thiago

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Thiago Venancio | 27 Feb 19:21 2015
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frac_identical | Bio::Search::Tiling::MapTiling

Hi all,

Bio::Search::Tiling::MapTiling frac_identical() is calculating it over the total query length instead of the aligned length in a a BLASTN. Below is the code I am using:

while( my $hit = $result->next_hit ) {
     my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
     my $id = $tiling->frac_identical(-type => 'query', -action => 'exact');
}

Does anyone know how to change this behavior ?

Best,
Thiago




! iv>
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Raoul J P Bonnal | 23 Feb 09:51 2015

OBF GSoC Registration

Please all possible mentors,

register yourself

https://www.google-melange.com/gsoc/homepage/google/gsoc2015

and try to connect to the organization Open Bioinformatics Foundation
id: obf

in case you are aware that some mentor can not be reached by this 
message feel free to forward it.

Best,
--
Ra & Fra

On 2/20/15 8:51 PM, Raoul Bonnal wrote:
> Dear All,
> I have created a special section
>
>
> http://www.open-bio.org/wiki/Google_Summer_of_Code#Scientific_Achievements
>
> I think that would be very useful to add all the references where GSoC has been used for doing science.
>
>
> please go ahead and add your project/paper/or whatever you think that google should know about our work.
>
>
> --
> Ra
Fields, Christopher J | 14 Feb 05:38 2015

Google Summer of Code 2015

All,

OBF and The Perl Foundation are both working on reapplying for the Google Summer of Code.  Note that we will
gladly accept Perl 6 related projects as well!  

Here is the spot for OBF-specific project ideas:

 http://www.open-bio.org/wiki/Google_Summer_of_Code

Perl-related ones can also be added here:

 http://blogs.perl.org/users/shadowcat_mdk/2015/02/gsoc-2015.html
 http://wiki2.enlightenedperl.org/index.php5?title=2015_Ideas_Page

chris
Weigang Qiu | 6 Feb 21:37 2015
Picon

Re: Bb-utils

Dear BP developers,

We have packaged the initial release (1.0) of bp-utils, which contains two bioperl-based utilities: "bioseq" and "bioaln" (another two utilities, "biopop" and "biotree", are in pre-release cleaning-up)

https://github.com/bioperl/bp-utils/blob/master/bp-utils-current-release.tar.gz

For project description, rationale, and call for developers, please see:

https://github.com/bioperl/bp-utils/blob/master/README.md

Thanks Chris and other for setting up the github access. Please feel free to email me for any feedback and bugs.

cheers,

--
Weigang Qiu


On Fri, Dec 12, 2014 at 9:59 PM, Fields, Christopher J <cjfields <at> illinois.edu> wrote:
Hi Weigang,

I wonder whether it would be better to have a separate bputils repo in the BioPerl space.  This would allow development to continue w/o tying it directly to a release, and I think would solve the exposure problem much more so than having it included in the main bioperl-live repo.  We could also feasibly include it as part of the main CPAN bioperl release, maybe by simply linking to it as a git submodule and packaging it up.

chris

On Dec 9, 2014, at 3:01 PM, Weigang Qiu <weigangq <at> gmail.com> wrote:

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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--
Weigang Qiu
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Mark A. Jensen | 26 Jan 15:23 2015
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Conversion of Phred 33 -> Phred 64 quality

Hi folks,
I know I could RTFM, but maybe someone knows off the top of their head: 
I understand that Illumina at one time made a switch in the constant 
added to quality scores to generate the FASTQ that comes off their 
instruments. This leads to a certain incomparability of data before and 
after that switch. This is about all I know of the issue; does anyone 
here have experience with this? Are there any BP modules that do this 
translation?
much appreciated-
MAJ
Shane McCoy | 14 Jan 00:23 2015
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Properly installing Bioperl - Ubuntu - Git

Hello! 
Not too familiar w/ Bioperl and want to make sure i've properly installed on my VM ubuntu 14.4 server w/ git. 

sudo apt-get update
sudo apt-get upgrade
sudo apt-get check
sudo apt-get autoclean

sudo apt-get install build-essential git gcc
sudo apt-get install libexpat1 expat
sudo apt-get install libgd-dev  (unable to locate libgd recommended on gmod.org/wiki/BioPerl Dependencies Outside perl)
sudo apt-get install libssl-dev
sudo apt-get install libpq-dev
sudo apt-get install libdb-dev libperl-dev
sudo apt-get install libgd-gd2-perl
sudo apt-get install libxml2
sudo apt-get install libxml2-dev

Installed local::lib manually for perl modules. Set environment path 
echo '[ $SHLVL -eq 1 ] && eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >>~/.bashrc

cpan> install Bundle::CPAN (archive::zip failed? pff!) 
cpan> install Bundle::BioPerl
Failed during this command:
 LDS/AcePerl-1.92.tar.gz                      : make_test NO
 CJFIELDS/Bio-ASN1-EntrezGene-1.70.tar.gz     : make_test NO
 CAPTTOFU/DBD-mysql-4.029.tar.gz              : writemakefile NO '/usr/bin/perl Makefile.PL 
and several more. missing packages etc and successfully installed except the above 3. Don't think i need those.

sudo apt-get install libgd-gd2-perl

cd bioperl-live 
 
perl Build.PL 
--fails - needs more modules


Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL
Checking prerequisites...
  recommends:

Algorithm::Munkres 
Array::Compare 
Bio::Phylo 
Convert::Binary::C 
GraphViz
HTML::TableExtract is not installed
PostScript::TextBlock is not installed
SOAP::Lite 
Net::SSLeay Crypt::SSLeay IO::Socket::SSL
Sort::Naturally 
XML::LibXML 
DBD::Pg 
DBD::SQLite
(all above installed via CPAN)

Checking optional features...
EntrezGene............disabled
  requires:
    ! Bio::ASN1::EntrezGene is not installed
 - starts installing bioperl 
i let it run and it installed Bioperl fine via CPAN.  build OK. 
Installed bio::asn1::entrezgene & bio::root::build
perl Build.PL
now needs Inline::C...
cpan>install Inline::C
 cd bioperl-live 

 perl Build.PL 
 -- fails. missing Manifest?
Build manifest
perl Build.PL --still fails
perl Build -- works
./Build test 
 --PASS
sudo ./Build install 

Installed / passed tests OK. 
Added;
export PERL5LIB="$HOME/bioperl-live:$PERL5LIB"
to .bashrc

So i've installed via CPAN which i didn't really want, but couldn't run Build.PL w/o prereq Bio::ASN1::EntrezGene which starts installing bioperl. What should i have done differently? 
i still did Build w/ Git clone, but when i check Version i get 1.006924. I thought the bioperl-live version was 1.006925? i set the environment variable in bashrc for bioperl-live. 
Ok, thanks for your time! Just want to make sure i'm doing this correctly. 
Shane
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Gmane