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The BED file spec says that strand given as '.' is unstranded but when parsed I am seeing that it is -1

test.pl

use Bio::FeatureIO;
use Data::Dumper;

my $io = Bio::FeatureIO->new(
    -format => 'bed',
    -file => 'test.txt'
);

while ( my $f = $io->next_feature() ) {
    print $f->strand;
}

test.txt

NbV1Ch01	18776453	18777002	MACS2_peak_1486	34	.	2.35549	5.48617	3.42439	437

Possibly seeing problems with versions of Module::Build packaged with older versions of perl:

http://www.cpantesters.org/cpan/report/748624a6-32e5-11e4-a623-e0a6dfbfc7aa

After downloading a zipfile of Bio-FeatureIO from GitHub, I needed to install the following modules to get it to pass it's tests and install via:

cd /tmp/Bio-FeatureIO-master
cpanm .

Test::Warn
Exception::Class
Tree::DAG_Node
Test::Deep

I already had the current BioPerl from CPAN and various chado related bits (Bundle::Chado, Go-Perl) installed.

Some (all?) seem to be test phase dependencies. Maybe the dist.ini should use the Autoprereqs plugin?

gff.pm in 1.6 decodes strings in the wrong place, resulting in exception even if valid values.

GFF3 specification:

Target

Indicates the target of a nucleotide-to-nucleotide or protein-to-nucleotide alignment. The format of the value is "target_id start end [strand]", where strand is optional and may be "+" or "-". If the target_id contains spaces, they must be escaped as hex escape %20.

However, line 636 from gff.pm assigns a DECODED value to attr Target, converting valid %20 into spaces
So, Target='A%20B 1 23 +;' will be converted to $attr{'Target'} = 'A B 1 23 +' when it should keep the original value.
This brings problems when the value is parsed at line 706 (my ($t_id,$tstart,$tend,$strand,$extra) = split /\s+/, $target_string; ), resulting in an exception 'The value in the Target string, $target_string, does not conform to the GFF3 specification'

Author Name: Heikki Lehvaslaiho (@heikkil)
Original Redmine Issue: 2513, https://redmine.open-bio.org/issues/2513
Original Date: 2008-06-10
Original Assignee: Bioperl Guts

A Bio::SeqFeature::Annotated object can not be created unless there is
a network connection. It tries to downloads a song SO.obo file from sourceforce. See the stack trace below.

Does this class really need to connect to network by default?

As a first fix, I’ve disabled running of tests in t/SeqFeatAnnotated.t
unless networked tests have been enabled.

-Heikki

P.S. I committed the temporary fix to tests in a wrong directory, so all the most recent POD fixes in bioperl-live got the comment meant for this fix.

——————————- WARNING ——————————-
MSG: [1/5] tried to fetch http://song.cvs.sourceforge.net/\*checkout\*/song/ontology/so.obo?rev=HEAD, but server threw 500. retrying…
—————————————————————————-
signalled

——————- EXCEPTION: Bio::Root::Exception ——————-
MSG: failed to fetch http://song.cvs.sourceforge.net/\*checkout\*/song/ontology/so.obo?rev=HEAD, server threw 500
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/heikki/src/bioperl-live/Bio/Root/Root.pm:357
STACK: Bio::Root::IO::_initialize_io /home/heikki/src/bioperl-live/Bio/Root/IO.pm:272
STACK: Bio::OntologyIO::_initialize /home/heikki/src/bioperl-live/Bio/OntologyIO.pm:187
STACK: Bio::OntologyIO::obo::_initialize /home/heikki/src/bioperl-live/Bio/OntologyIO/obo.pm:137
STACK: Bio::OntologyIO::new /home/heikki/src/bioperl-live/Bio/OntologyIO.pm:162
STACK: Bio::OntologyIO::new /home/heikki/src/bioperl-live/Bio/OntologyIO.pm:171
STACK: Bio::Ontology::OntologyStore::get_ontology /home/heikki/src/bioperl-live/Bio/Ontology/OntologyStore.pm:225
STACK: Bio::SeqFeature::Annotated::primary_tag /home/heikki/src/bioperl-live/Bio/SeqFeature/Annotated.pm:656
STACK: Bio::SeqFeature::Annotated::_initialize /home/heikki/src/bioperl-live/Bio/SeqFeature/Annotated.pm:244
STACK: Bio::SeqFeature::Annotated::new /home/heikki/src/bioperl-live/Bio/SeqFeature/Annotated.pm:210
STACK: t/SeqFeatAnnotated.t:16

Author Name: Keith James (Keith James)
Original Redmine Issue: 2429, https://redmine.open-bio.org/issues/2429
Original Date: 2008-01-03
Original Assignee: Bioperl Guts

I was getting this error from all my GFF3 files:

——————- EXCEPTION: Bio::Root::Exception ——————-
MSG: Oops! ID cds00001 exists more than once in your file!
STACK: Error::throw
STACK: Bio::Root::Root::throw /software/perl-5.8.8/lib/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::FeatureIO::gff::next_feature_group /software/perl-5.8.8/lib/site_perl/5.8.8/Bio/FeatureIO/gff.pm:206

Several code comments within Bio/FeatureIO/gff.pm indicate that it assumes an unique ID for each line. The spec states that an ID must be unique within a file, but one assumes that this means unique /per feature/ where a feature may be split over several lines. The example GFF in the spec supports this interpretation.

To confirm the bug I created a copy of the canonical GFF3 example from the spec and reproduced this error (see above); the cds00001 feature is split over 4 lines, each with the same ID.

This is with bioperl release bioperl-1.5.2_102 on Linux i686, Perl v5.8.8

Bio::SeqFeature::Annotated requires Bio::Ontology updates (which load in so.obo from a remote URL). These can also be moved into a release test if needed.

I am a newbee. I have failed to install Bio-FeatureIO on Ubuntu 16 LTS following;

sudo cpan
install CPAN
reload cpan
install Bio::FeatureIO::gff

even trying to download the source code has failed since I cannot find the Build.PL file
Thanks

Author Name: Chris Fields (@cjfields)
Original Redmine Issue: 2763, https://redmine.open-bio.org/issues/2763
Original Date: 2009-02-17
Original Assignee: Bioperl Guts

Simple tracker for proposed Bio::FeatureIO refactoring. This will also include a refactor of Bio::SeqFeature::Annotated.

$feature->name is not initialised when reading a bed file.

Below is an example describing the issue.

With the following bed file called example.bed

chr1        0       98      Pos1 

And the following perl script called test1.pl

#!/usr/bin/env perl

use strict;
use warnings;

use Bio::FeatureIO;

my $featureIO = Bio::FeatureIO->new(-file=>"example.bed",-format=>'bed');

my $feature = $featureIO->next_feature;

print $feature->name."\n";

On execution I get the following output.

Use of uninitialized value in print at test1.pl line 12

With the following perl script called test2.pl

#!/usr/bin/env perl

use strict;
use warnings;

use Bio::FeatureIO;

my $featureIO = Bio::FeatureIO->new(-file=>"example.bed",-format=>'bed');

my $feature = $featureIO->next_feature;

print $feature->get_tag_values('Name')."\n";

On execution I get the following output.

Pos1