[Bioperl-l] Bio::SeqFeature::Generic

[Charles Hauser]

Don't know if this is a bug or a problem on my end.

Using Bio::SeqFeature::Generic to generate gff:

	my $feat = new Bio::SeqFeature::Generic();
	$feat->seq_id($seq->id);
	$feat->source_tag('assembly');
	$feat->primary_tag('contig');
	$feat->start('1');
	$feat->end($seq->length);
	$feat->add_tag_value('Contig',$seq->id);
	$out->write_feature($feat);

I end up with 2 extra spaces following the group tag ('Contig
scaffold_1') which results in gbrowse returning: ...landmark not
recognized...

deleting these spaces makes all right with the world.

Is the problem in my code or in  Bio::SeqFeature::Generic?

Charles

-------------- next part --------------
scaffold_1	assembly	contig	1	2159858	.	.	.	Contig scaffold_1  
scaffold_1	ace	match	50886	52846	.	+	.	Target "ACE:20021010.8753.1"  9 687  
scaffold_1	ace	HSP	50886	51245	.	+	.	Target "ACE:20021010.8753.1"  9 368  
scaffold_1	ace	HSP	51578	51703	.	+	.	Target "ACE:20021010.8753.1"  369 494  
scaffold_1	ace	HSP	52280	52345	.	+	.	Target "ACE:20021010.8753.1"  495 560  
scaffold_1	ace	HSP	52719	52834	.	+	.	Target "ACE:20021010.8753.1"  561 676  
scaffold_1	ace	HSP	52836	52846	.	+	.	Target "ACE:20021010.8753.1"  677 687  
scaffold_1	ace	match	2852	3829	.	+	.	Target "ACE:20021010.432.1"  948 1577  
scaffold_1	ace	HSP	2852	2998	.	+	.	Target "ACE:20021010.432.1"  948 1094  
scaffold_1	ace	HSP	3175	3218	.	+	.	Target "ACE:20021010.432.1"  1095 1138  
scaffold_1	ace	HSP	3219	3305	.	+	.	Target "ACE:20021010.432.1"  1140 1226  
scaffold_1	ace	HSP	3479	3829	.	+	.	Target "ACE:20021010.432.1"  1227 1577  
scaffold_1	ace	match	47657	48119	.	+	.	Target "ACE:20021010.1025.1"  5 484  
scaffold_1	ace	HSP	47657	47746	.	+	.	Target "ACE:20021010.1025.1"  5 94  
scaffold_1	ace	HSP	47747	48119	.	+	.	Target "ACE:20021010.1025.1"  112 484  
scaffold_1	ace	match	44560	45221	.	+	.	Target "ACE:20021010.3151.1"  8 669  
scaffold_1	ace	HSP	44560	45221	.	+	.	Target "ACE:20021010.3151.1"  8 669  
scaffold_1	ace	match	47550	50747	.	+	.	Target "ACE:20021010.8359.1"  9 1212  
scaffold_1	ace	HSP	47550	48210	.	+	.	Target "ACE:20021010.8359.1"  9 669  
scaffold_1	ace	HSP	48741	48862	.	+	.	Target "ACE:20021010.8359.1"  670 791  
scaffold_1	ace	HSP	49384	49502	.	+	.	Target "ACE:20021010.8359.1"  792 910  
scaffold_1	ace	HSP	50261	50383	.	+	.	Target "ACE:20021010.8359.1"  911 1033  
scaffold_1	ace	HSP	50569	50747	.	+	.	Target "ACE:20021010.8359.1"  1034 1212