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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Demian Riccardi | 13 Jan 15:52 2015
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HackaMol 0.01 released

Hello BioPerl community!

HackaMol 0.01 has been released.  The library, very much inspired by BioPerl, targets structural analysis and multiscale molecular modeling. 

While this is an early release, I've pushed it as far as I could over the past year. There are surely areas that need work.  Contributions are welcome!  

  

Demian


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Carnë Draug | 9 Jan 01:04 2015
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bioperl executables files and dist-zilla

Hi

when installing new bioperl modules with dist zilla, the executable files
are not being installed.  The reason is that our dist zilla plugin bundle [1]
is searching for them in the default directory "bin/" while bioperl seems
to have them in a "scripts/" directory.  This is done by the ExecFiles plugin.

I can change this easily or I can just move the binaries to "bin/" (which
I think is more common).  Also, dropping the file extensions would make
things simpler.

One last thing, I was thinking of adding the SetScriptShebang plugin [3]
to the bundle. Opinions?

Carnë

[1] https://metacpan.org/pod/Pod::Weaver::PluginBundle::BioPerl
[2] https://metacpan.org/pod/Dist::Zilla::Role::ExecFiles
[2] https://metacpan.org/pod/Dist::Zilla::Plugin::SetScriptShebang

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Zakariyya Mughal | 24 Dec 06:01 2014
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A fast and natural interface to R from Perl

Hi everyone,

I have uploaded modules for working with the R interpreter from Perl.
The CPAN links are below, but to get a taste of what the API
looks like, check out my blog post <http://enetdown.org/dot-plan/posts/2014/12/24/a_fast_and_natural_interface_to_R_from_Perl/>.

- Statistics::NiceR <http://p3rl.org/Statistics::NiceR>
- Data::Frame <http://p3rl.org/Data::Frame>

I'd love to have feedback on how to improve them.

Regards and happy hacking,
- Zaki Mughal
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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Gmane