Bio::FeatureIO::bed, feature->name doesn't populate correctly

[ericenns]

$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

[bosborne]

Eric,

I see you entered this is as a bug, thank you for doing that.

We will take a look ….

Brian O.

On Nov 24, 2014, at 10:16 AM, ericenns [email protected] wrote:

$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
—
Reply to this email directly or view it on GitHub #6.

[bosborne]

Eric,

For the moment you can get that detail using display_name().

The problem, I guess, is that the specifications out there in the Web don’t talk about “display name” in field 4, they talk about “name”.

Brian O.

On Nov 24, 2014, at 10:16 AM, ericenns [email protected] wrote:

$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
—
Reply to this email directly or view it on GitHub #6.

[ericenns]

Brian,

I tested $feature->display_name() and it gave me the same behaviour as $feature->name(), meaning I also got uninitialized value.

Note I am using Perl v5.20.1 and the lastest version of Bio::FeatureIO

Eric

[bosborne]

Eric,

display_name() seems to be working in the latest code from github (https://github.com/bioperl/Bio-FeatureIO https://github.com/bioperl/Bio-FeatureIO). What code are you using?

Brian O.

On Nov 24, 2014, at 5:07 PM, ericenns [email protected] wrote:

Brian,

I tested $feature->display_name() and it gave me the same behaviour as $feature->name(), meaning I also got uninitialized value.

Eric

—
Reply to this email directly or view it on GitHub #6 (comment).

[ericenns]

Brian,

1.6.905, I installed from cpan.

Eric