Fields, Christopher J | 13 Apr 21:48 2015

Re: Problems installing on Mac OS 10.9.5

Seem you are installing to the system perl (see the ‘Permission denied’ issue).   You can install using ‘sudo’ but I highly suggest not installing this into your system Perl if possible, namely b/c it can cause problems down the road.  You should look into using homebrew to install a localized perl, then use that new version.  

Alternatively, you can use perlbrew (which I highky recommend as you can install multiple perl versions locally if needed):


chris

On Apr 13, 2015, at 2:16 PM, Mgavi Brathwaite <lsbrath <at> gmail.com> wrote:

Hi Chris,

I've done the install from CPAN and at the end of the install I'm informed that nothing installed.

Check attachment<Screen Shot 2015-04-13 at 3.15.01 PM.png>

On Sun, Apr 12, 2015 at 11:03 AM, Fields, Christopher J <cjfields <at> illinois.edu> wrote:
You’ll have to be more specific than that.  What specific problems did you encounter?  

chris

On Apr 12, 2015, at 12:21 AM, Mgavi Brathwaite <lsbrath <at> gmail.com> wrote:

Having difficulty installing BioPerl on my MacOS 10.9.5. Any suggestions?

Brath

-- 
Mgavi Elombe Brathwaite, MSc.
"Felix qui nihil debet"
"Happy is he who owes nothing"
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-- 
Mgavi Elombe Brathwaite, MSc.
"Felix qui nihil debet"
"Happy is he who owes nothing"

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Mgavi Brathwaite | 12 Apr 07:21 2015
Picon

Problems installing on Mac OS 10.9.5

Having difficulty installing BioPerl on my MacOS 10.9.5. Any suggestions?

Brath

--
Mgavi Elombe Brathwaite, MSc.
"Felix qui nihil debet"
"Happy is he who owes nothing"
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Adam Sjøgren | 9 Apr 14:47 2015
X-Face

EMBL file with space before quoted, multi-line qualifier value

  Hi.

I just stumbled over an EMBL file that has space after equal-sign that
follows the qualifier name.

BioPerl doesn't parse folded lines when that happens, because the "-char
is expected to be the first character after the '='.

I have whittled it down to this example:

ID   TEST standard; DNA; 10 BP.
XX
AC   TEST;
XX
DT   09-APR-2015
XX
DE   Test of space before quoted qualifier.
XX
XX
FH   Key             Location/Qualifiers
FT   CDS             1..10
FT                   /*tag= x
FT                   /gene= "someT"
FT                   /product= "somewordandt extthatisquite lon
FT                   gandthereforewraps"
XX
SQ   Sequence 10 BP; 10 A; 0 C; 0 G; 9 T; 0 U; 0 Other;
     aaaaaaaaaa       10
//

And this "one"-liner:

  ~$ perl -e 'use warnings; use strict; use Bio::SeqIO; my
$in=Bio::SeqIO->new("-file"=>"white_space.embl", "-format"=>"embl"); my $seq=$in->next_seq;
foreach my $feature ($seq->all_SeqFeatures) { print $feature->primary_tag . "\n"; map { print "  /" . $_ .
"=" . (join " ", $feature->get_tag_values($_)) . "\n"; } $feature->get_all_tags }'

  ------------- EXCEPTION: Bio::Root::Exception -------------
  MSG: Can't see new qualifier in: gandthereforewraps"
  from:
  /*tag= x
  /gene= "someT"
  /product= "somewordandt extthatisquite lon
  gandthereforewraps"

  STACK: Error::throw
  STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
  STACK: Bio::SeqIO::embl::_read_FTHelper_EMBL /usr/share/perl5/Bio/SeqIO/embl.pm:1361
  STACK: Bio::SeqIO::embl::next_seq /usr/share/perl5/Bio/SeqIO/embl.pm:400
  STACK: -e:1
  -----------------------------------------------------------

shows the error.

If I add this patch:

--- Bio/SeqIO/embl.pm.orig	2015-04-09 14:27:08.035573910 +0200
+++ Bio/SeqIO/embl.pm	2015-04-09 14:27:46.952373300 +0200
 <at>  <at>  -1358,7 +1358,7  <at>  <at> 
     # intact to provide informative error messages.)
   QUAL: for (my $i = 0; $i <  <at> qual; $i++) {
         $_ = $qual[$i];
-        my( $qualifier, $value ) = m{^/([^=]+)(?:=(.+))?}
+        my( $qualifier, $value ) = m{^/([^=]+)*(?:=\s*(.+))?}
             or $self->throw("Can't see new qualifier in: $_\nfrom:\n"
                             . join('', map "$_\n",  <at> qual));
         if (defined $value) {

then the output is:

  CDS
    /*tag=x
    /gene=someT
    /product=somewordandt extthatisquite lon gandthereforewraps

which seems more reasonable, even if the format does not allow
whitespace after the =-sign (I haven't checked).

What do you think?

  Best regards,

    Adam

--

-- 
                                                          Adam Sjøgren
                                                    adsj <at> novozymes.com

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Wilson, Colin (CC | 4 Mar 01:13 2015
Picon

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";
}
lawrence.benbow | 14 Mar 15:04 2015
Picon

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
Picon

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

Gmane