[Bioperl-l] confused by Bio::Graphics

richard rbirnie at totalise.co.uk
Sun Dec 3 16:38:02 EST 2006

Hi all,

I'm having a little trouble getting Bio::Graphics to give me the correct 
output and I'm looking for some help. I am trying to extend from example 5 of 
the Graphics HOWTO on the bioperl wiki using version 1.4 of Bioperl. 
Eventually I intend the script to follow example 6 but I thought I'd try the 
simpler version first.

The basic aim of the script is that it takes as input a file containing a list 
of GenBank IDs plus some other info for alternative transcripts of a gene. 
This information is stored in a hash and the GenBank IDs are used to retrieve 
the appropriate entries from GenBank. I then want to use Bio::Graphics to 
generate a figure from the feature tables showing the CDSs from the 
alternative transcripts. 

So far I have managed to retrieve the GenBank entries extract the feature 
tables and store a reference to these in the hash mentioned above. I've also 
got Bio::Graphics to draw a basic image but some of the details aren't right 
and I don't understand why. I have attached the code I have so far, the input 
file and the output image to this mail. I didn't want to display it all in 
the main message but I'm not actually sure which bit is causing the problem. 
The code is very rough and in need of polishing but I need to get it to work 
correctly first.

These are the problems:
1) As I understand it this:

my $wholeseq = Bio::SeqFeature::Generic->new (
		-start => 1,
		-end => $refseq->length,
		-display_name =>$refseq->display_name

should display the name of the gene (CD133/Prominin1) near the top of image. 
It doesn't, am I misunderstanding or is there an error in the code?

2) In the quoted example the CDS is broken up into smaller regions which are 
then linked together in example 6. This isn't happening in my code and I 
think it should be, I get one solid block for the CDS. I don't understand why 
this is because I'm not clear which parts of the feature table are used to 
define where the CDS should be split. I think this is the relevant bit of 

foreach my $alt_trans (keys %main) {
	foreach my $tag (keys %{ $main{$alt_trans}{'features'} }) {

		my $feature = $main{$alt_trans}{'features'}{$tag};

				-glyph => 'generic',
				-bgcolor => $colors[$idx++ % @colors],
				-fgcolor => 'black',
				-font2color => 'black',
				-key => $alt_trans,
				-bump => +1,
				-height => 8,
				-label => 1,
				-description => 1,
				) if ($tag eq 'CDS');


Can anyone tell me what I am doing wrong?

RefSeq entry for the gene of interest is here:
If I understand correctly the example file used in the HOWTO is this gene:

Final question, does bioperl come with example scripts and is so where whould 
they normally be found on a Linux system?

If anyone is still reading this thanks for your patience. Any clarification 
will be appreciated.

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sequence_ID	Exon_Boundary	Assay_location	Amplicon_length
NM_006017	9 - 10	1118	106
AF027208.1	9 - 10	1118	106
AK027420.1	9 - 10	1312	106
AK027422.1	9 - 10	1334	106
BC012089.1	9 - 10	1289	106
AY449689.1	8 - 9	1054	106
AY449690.1	8 - 9	1054	106
AY449691.1	8 - 9	1054	106
AY449692.1	9 - 10	1081	106
AY449693.1	9 - 10	1081	106
AF507034.1	8 - 9	1091	106
AK075411.1	9 - 10	1289	106
AF117225.1	9 - 10	1334	106
AK226033.1	-	1312	106
DQ895452.1	-	1054	106
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