Hi all,
I've just upgraded to 1.69 from 1.67 very successfully and compliments
to all involved.
My little gripe is the functionality of the gene.pm
We've got a genes file containing no UTR or CDS (see below), just mRNA
and exons.
Setting 'sub_part = exon' worked a treat for displaying alternate exon
structure in transcripts for 1.67
I'm just getting one big generic block spanning the transcript in the
new version
I've included conf and a little of the file below.
Sean.
[Hs.hek]
feature = gene:Solexa_subexons
glyph = gene
sub_part = exon # if no utr's or cds are in the file
fgcolor = black
bgcolor = dodgerblue
height = 10
label_transcripts = 1
connector = 1
pad_left = 50
category = Genes
linewidth = 1
key = hek_hugues
label = sub{
my $feature = shift;
my $label = join(' ', $feature->each_tag_value("Alias"));
return $label;
}
description = 1
##gff-version 3
chr20 Solexa_subexons gene 48984811 49008494 .
- .
ID=ENSG00000000419;ensembl_id=ENSG00000000419;Note=Total.count:135-Niter:262
chr20 Solexa_subexons mRNA 48984811 49008494 .
- .
ID=ENST00000371584;Parent=ENSG00000000419;ensembl_id=ENST00000371584;Alias=0.104
chr20 Solexa_subexons exon 48984811 48985180 .
- . ID=ENST00000371584_E1;Parent=ENST00000371584
chr20 Solexa_subexons exon 48986092 48986206 .
- . ID=ENST00000371584_E2;Parent=ENST00000371584
chr20 Solexa_subexons exon 48990809 48990877 .
- . ID=ENST00000371584_E3;Parent=ENST00000371584
chr20 Solexa_subexons exon 48991049 48991072 .
- . ID=ENST00000371584_E4;Parent=ENST00000371584
chr20 Solexa_subexons exon 48991073 48991153 .
- . ID=ENST00000371584_E5;Parent=ENST00000371584
chr20 Solexa_subexons exon 48991975 48992070 .
- . ID=ENST00000371584_E6;Parent=ENST00000371584
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